rtracklayer: Problems running vignette
1
0
Entering edit mode
Simon Anders ▴ 150
@simon-anders-2626
Last seen 7.9 years ago
Hi Michael, I've just tried to use rtracklayer, following your vignette, and ran into two problems. 1. I cannot add any tracks to a session. I entered the code in the vignette to produce the "targets" track and exported it as "targets.bed". To make things easier to follow, let's say, I start from there with a fresh R session: library(rtracklayer) # Import the data targets <- import("targets.bed") # targets is now a RangedData object with 3052 ranges and # sequence names chr1 chr10 chr11 chr12 ... # Create a session session <- browserSession("UCSC") # Add the 'targets' track to the session: track(session, "MYTRACK") <- targets Is this last command correct? It does not produce an error, but it does not seem to do anything, either. If I list all the tracks in the session with trackNames(session) I get a list of 196 UCSC standard tracks, but "MYTRACK" is not mentioned. How do I correctly add a track? 2. There is some mangling happening with the chromosome names. The man page for 'browserView' suggests to try: browserView(session, GenomicRanges(20000, 50000, "chr2")) Doing this asks my web browser to open the following URL: http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 Note that it says "chrchr2", i.e., a superfluous "chr" got prefixed to the sequence name. Obviously, the UCSC page cannot deal with this and one gets an error message displayed by JavaScript that "chrchr2" is not known. I run into the same problem if I follow the vignette's code to demonstrate 'browserView'. If I try browserView(session, GenomicRanges(20000, 50000, "2")) I get the range chr2:20000-50000 correctly displayed in my web browser. There is, however, still now sight of "MYTRACK". What's going wrong here? > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.4.0 RCurl_0.94-1 loaded via a namespace (and not attached): [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0 [5] XML_2.3-0 Cheers Simon +--- | Dr. Simon Anders, Dipl. Phys. | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK | office phone +44-1223-492680, mobile phone +44-7505-841692 | preferred (permanent) e-mail: sanders at fs.tum.de
rtracklayer rtracklayer • 1.1k views
ADD COMMENT
0
Entering edit mode
@michael-lawrence-2759
Last seen 7.9 years ago
On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders@ebi.ac.uk> wrote: > Hi Michael, > > I've just tried to use rtracklayer, following your vignette, and ran into > two problems. > > > 1. I cannot add any tracks to a session. > > I entered the code in the vignette to produce the "targets" track and > exported it as "targets.bed". To make things easier to follow, let's say, I > start from there with a fresh R session: > > library(rtracklayer) > > # Import the data > targets <- import("targets.bed") > # targets is now a RangedData object with 3052 ranges and > # sequence names chr1 chr10 chr11 chr12 ... > > # Create a session > session <- browserSession("UCSC") > > # Add the 'targets' track to the session: > track(session, "MYTRACK") <- targets > > Is this last command correct? It does not produce an error, but it does not > seem to do anything, either. If I list all the tracks in the session with > trackNames(session) > I get a list of 196 UCSC standard tracks, but "MYTRACK" is not mentioned. > > How do I correctly add a track? > Well, I can say that this works for me. I need to look into parsing the error messages returned by UCSC. You can always try uploading to UCSC manually to see what went wrong. I know that back in December the BED output was mishandling the score values. > > > 2. There is some mangling happening with the chromosome names. > > The man page for 'browserView' suggests to try: > > browserView(session, GenomicRanges(20000, 50000, "chr2")) > > Doing this asks my web browser to open the following URL: > > > http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 > > Note that it says "chrchr2", i.e., a superfluous "chr" got prefixed to the > sequence name. Obviously, the UCSC page cannot deal with this and one gets > an error message displayed by JavaScript that "chrchr2" is not known. > > I run into the same problem if I follow the vignette's code to demonstrate > 'browserView'. > > If I try > browserView(session, GenomicRanges(20000, 50000, "2")) > I get the range chr2:20000-50000 correctly displayed in my web browser. > There is, however, still now sight of "MYTRACK". > > What's going wrong here? > Thanks for pointing this out. I've fixed this for version 1.5.3. Michael > > > > sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.4.0 RCurl_0.94-1 > > loaded via a namespace (and not attached): > [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0 > [5] XML_2.3-0 > > > Cheers > Simon > > > +--- > | Dr. Simon Anders, Dipl. Phys. > | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK > | office phone +44-1223-492680, mobile phone +44-7505-841692 > | preferred (permanent) e-mail: sanders@fs.tum.de > > > > [[alternative HTML version deleted]]
ADD COMMENT
0
Entering edit mode
Hi Michael, I get the same results as Simon. In fact, if I source() the vignette code and then run some of the chunks that are set to eval=false, I get errors: > source("c:/R-2.9.0/library/rtracklayer/doc/rtracklayer.R") Loading required package: hgu133plus2.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: Biostrings Loading required package: IRanges [snip] > session <- browserSession("UCSC") > track(session, "targets") <- targetTrack > targetTrack RangedData: 3063 ranges by 3 columns columns(3): strand name target sequences(23): chr1 chr10 chr11 chr12 chr13 ... chr7 chr8 chr9 chrX > view <- browserView(session, range(targetTrack)*-10, pack="targets") Error in validObject(x) : invalid class "IRanges" object: the widths must be non-NA integers In addition: Warning message: In numeric2integer(value) : NAs introduced by coercion Error in ucscForm(range) : error in evaluating the argument 'object' in selecting a method for function 'ucscForm' > view <- browserView(session, range(subTargetTrack) * -10,pack = "targets") Error in resolveTrackIndex(x, i) : Unknown tracks:targets If I export targetTrack as a bedfile and upload to UCSC I get no errors and can view the track without problems. On another subject, you might consider replacing the plot of the cpneTrack in the vignette with a .png rather than a .pdf. Trying to scroll through the vignette is a real drag when you get to that plot. > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods [7] base other attached packages: [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 [2] BSgenome_1.12.2 [3] rtracklayer_1.4.0 [4] RCurl_0.97-3 [5] bitops_1.0-4.1 [6] org.Hs.eg.db_2.2.11 [7] microRNA_1.2.0 [8] Rlibstree_0.3-2 [9] Biostrings_2.12.4 [10] IRanges_1.2.2 [11] genefilter_1.24.2 [12] humanStemCell_0.2.0 [13] hgu133plus2.db_2.2.11 [14] RSQLite_0.7-1 [15] DBI_0.2-4 [16] AnnotationDbi_1.6.0 [17] affy_1.22.0 [18] Biobase_2.4.1 [19] limma_2.18.1 [20] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] affyio_1.12.0 annotate_1.22.0 preprocessCore_1.6.0 [4] splines_2.9.0 survival_2.35-4 tools_2.9.0 [7] XML_2.3-0 xtable_1.5-5 Best, Jim Michael Lawrence wrote: > On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders at="" ebi.ac.uk=""> wrote: > >> Hi Michael, >> >> I've just tried to use rtracklayer, following your vignette, and ran into >> two problems. >> >> >> 1. I cannot add any tracks to a session. >> >> I entered the code in the vignette to produce the "targets" track and >> exported it as "targets.bed". To make things easier to follow, let's say, I >> start from there with a fresh R session: >> >> library(rtracklayer) >> >> # Import the data >> targets <- import("targets.bed") >> # targets is now a RangedData object with 3052 ranges and >> # sequence names chr1 chr10 chr11 chr12 ... >> >> # Create a session >> session <- browserSession("UCSC") >> >> # Add the 'targets' track to the session: >> track(session, "MYTRACK") <- targets >> >> Is this last command correct? It does not produce an error, but it does not >> seem to do anything, either. If I list all the tracks in the session with >> trackNames(session) >> I get a list of 196 UCSC standard tracks, but "MYTRACK" is not mentioned. >> >> How do I correctly add a track? >> > > Well, I can say that this works for me. I need to look into parsing the > error messages returned by UCSC. You can always try uploading to UCSC > manually to see what went wrong. I know that back in December the BED output > was mishandling the score values. > > >> >> 2. There is some mangling happening with the chromosome names. >> >> The man page for 'browserView' suggests to try: >> >> browserView(session, GenomicRanges(20000, 50000, "chr2")) >> >> Doing this asks my web browser to open the following URL: >> >> >> http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 >> >> Note that it says "chrchr2", i.e., a superfluous "chr" got prefixed to the >> sequence name. Obviously, the UCSC page cannot deal with this and one gets >> an error message displayed by JavaScript that "chrchr2" is not known. >> >> I run into the same problem if I follow the vignette's code to demonstrate >> 'browserView'. >> >> If I try >> browserView(session, GenomicRanges(20000, 50000, "2")) >> I get the range chr2:20000-50000 correctly displayed in my web browser. >> There is, however, still now sight of "MYTRACK". >> >> What's going wrong here? >> > > Thanks for pointing this out. I've fixed this for version 1.5.3. > > Michael > > >> >>> sessionInfo() >> R version 2.9.0 (2009-04-17) >> x86_64-unknown-linux-gnu >> >> locale: >> >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en _GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] rtracklayer_1.4.0 RCurl_0.94-1 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0 >> [5] XML_2.3-0 >> >> >> Cheers >> Simon >> >> >> +--- >> | Dr. Simon Anders, Dipl. Phys. >> | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK >> | office phone +44-1223-492680, mobile phone +44-7505-841692 >> | preferred (permanent) e-mail: sanders at fs.tum.de >> >> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLY
0
Entering edit mode
On Thu, Jun 4, 2009 at 7:03 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Michael, > > I get the same results as Simon. In fact, if I source() the vignette code > and then run some of the chunks that are set to eval=false, I get errors: > > > source("c:/R-2.9.0/library/rtracklayer/doc/rtracklayer.R") > Loading required package: hgu133plus2.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: Biostrings > Loading required package: IRanges > [snip] > > > session <- browserSession("UCSC") > > track(session, "targets") <- targetTrack > > targetTrack > RangedData: 3063 ranges by 3 columns > columns(3): strand name target > sequences(23): chr1 chr10 chr11 chr12 chr13 ... chr7 chr8 chr9 chrX > > view <- browserView(session, range(targetTrack)*-10, pack="targets") > Error in validObject(x) : > invalid class "IRanges" object: the widths must be non-NA integers > In addition: Warning message: > In numeric2integer(value) : NAs introduced by coercion > Error in ucscForm(range) : > error in evaluating the argument 'object' in selecting a method for > function 'ucscForm' > > view <- browserView(session, range(subTargetTrack) * -10,pack = > "targets") > Error in resolveTrackIndex(x, i) : Unknown tracks:targets > > If I export targetTrack as a bedfile and upload to UCSC I get no errors and > can view the track without problems. > I'm kind of at a loss here. I have your same sessionInfo on my machine (fresh R install, everything via biocLite) and yet it seems to work just fine. What's your curl version? Mine is 7.19.4. Michael > > On another subject, you might consider replacing the plot of the cpneTrack > in the vignette with a .png rather than a .pdf. Trying to scroll through the > vignette is a real drag when you get to that plot. > Yes, good idea. > > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods > [7] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 > [2] BSgenome_1.12.2 > [3] rtracklayer_1.4.0 > [4] RCurl_0.97-3 > [5] bitops_1.0-4.1 > [6] org.Hs.eg.db_2.2.11 > [7] microRNA_1.2.0 > [8] Rlibstree_0.3-2 > [9] Biostrings_2.12.4 > [10] IRanges_1.2.2 > [11] genefilter_1.24.2 > [12] humanStemCell_0.2.0 > [13] hgu133plus2.db_2.2.11 > [14] RSQLite_0.7-1 > [15] DBI_0.2-4 > [16] AnnotationDbi_1.6.0 > [17] affy_1.22.0 > [18] Biobase_2.4.1 > [19] limma_2.18.1 > [20] biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 preprocessCore_1.6.0 > [4] splines_2.9.0 survival_2.35-4 tools_2.9.0 > [7] XML_2.3-0 xtable_1.5-5 > > Best, > > Jim > > > > Michael Lawrence wrote: > >> On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders@ebi.ac.uk> wrote: >> >> Hi Michael, >>> >>> I've just tried to use rtracklayer, following your vignette, and ran into >>> two problems. >>> >>> >>> 1. I cannot add any tracks to a session. >>> >>> I entered the code in the vignette to produce the "targets" track and >>> exported it as "targets.bed". To make things easier to follow, let's say, >>> I >>> start from there with a fresh R session: >>> >>> library(rtracklayer) >>> >>> # Import the data >>> targets <- import("targets.bed") >>> # targets is now a RangedData object with 3052 ranges and >>> # sequence names chr1 chr10 chr11 chr12 ... >>> >>> # Create a session >>> session <- browserSession("UCSC") >>> >>> # Add the 'targets' track to the session: >>> track(session, "MYTRACK") <- targets >>> >>> Is this last command correct? It does not produce an error, but it does >>> not >>> seem to do anything, either. If I list all the tracks in the session with >>> trackNames(session) >>> I get a list of 196 UCSC standard tracks, but "MYTRACK" is not mentioned. >>> >>> How do I correctly add a track? >>> >>> >> Well, I can say that this works for me. I need to look into parsing the >> error messages returned by UCSC. You can always try uploading to UCSC >> manually to see what went wrong. I know that back in December the BED >> output >> was mishandling the score values. >> >> >> >>> 2. There is some mangling happening with the chromosome names. >>> >>> The man page for 'browserView' suggests to try: >>> >>> browserView(session, GenomicRanges(20000, 50000, "chr2")) >>> >>> Doing this asks my web browser to open the following URL: >>> >>> >>> >>> http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 >>> >>> Note that it says "chrchr2", i.e., a superfluous "chr" got prefixed to >>> the >>> sequence name. Obviously, the UCSC page cannot deal with this and one >>> gets >>> an error message displayed by JavaScript that "chrchr2" is not known. >>> >>> I run into the same problem if I follow the vignette's code to >>> demonstrate >>> 'browserView'. >>> >>> If I try >>> browserView(session, GenomicRanges(20000, 50000, "2")) >>> I get the range chr2:20000-50000 correctly displayed in my web browser. >>> There is, however, still now sight of "MYTRACK". >>> >>> What's going wrong here? >>> >>> >> Thanks for pointing this out. I've fixed this for version 1.5.3. >> >> Michael >> >> >> >>> sessionInfo() >>>> >>> R version 2.9.0 (2009-04-17) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> >>> >>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=e n_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID ENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] rtracklayer_1.4.0 RCurl_0.94-1 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0 >>> [5] XML_2.3-0 >>> >>> >>> Cheers >>> Simon >>> >>> >>> +--- >>> | Dr. Simon Anders, Dipl. Phys. >>> | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK >>> | office phone +44-1223-492680, mobile phone +44-7505-841692 >>> | preferred (permanent) e-mail: sanders@fs.tum.de >>> >>> >>> >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
Michael Lawrence wrote: > > > On Thu, Jun 4, 2009 at 7:03 AM, James W. MacDonald > <jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu="">> wrote: > > Hi Michael, > > I get the same results as Simon. In fact, if I source() the vignette > code and then run some of the chunks that are set to eval=false, I > get errors: > > > source("c:/R-2.9.0/library/rtracklayer/doc/rtracklayer.R") > Loading required package: hgu133plus2.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: Biostrings > Loading required package: IRanges > [snip] > > > session <- browserSession("UCSC") > > track(session, "targets") <- targetTrack > > targetTrack > RangedData: 3063 ranges by 3 columns > columns(3): strand name target > sequences(23): chr1 chr10 chr11 chr12 chr13 ... chr7 chr8 chr9 chrX > > view <- browserView(session, range(targetTrack)*-10, pack="targets") > Error in validObject(x) : > invalid class "IRanges" object: the widths must be non-NA integers > In addition: Warning message: > In numeric2integer(value) : NAs introduced by coercion > Error in ucscForm(range) : > error in evaluating the argument 'object' in selecting a method for > function 'ucscForm' > > view <- browserView(session, range(subTargetTrack) * -10,pack = > "targets") > Error in resolveTrackIndex(x, i) : Unknown tracks:targets > > If I export targetTrack as a bedfile and upload to UCSC I get no > errors and can view the track without problems. > > > I'm kind of at a loss here. I have your same sessionInfo on my machine > (fresh R install, everything via biocLite) and yet it seems to work just > fine. What's your curl version? Mine is 7.19.4. I am on Windows, and am using the binary from BioC, so the curl version is whatever you guys are using to build the package with. I assume it is relatively new? Jim > > Michael > > > > On another subject, you might consider replacing the plot of the > cpneTrack in the vignette with a .png rather than a .pdf. Trying to > scroll through the vignette is a real drag when you get to that plot. > > > Yes, good idea. > > > > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods > [7] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 > [2] BSgenome_1.12.2 > [3] rtracklayer_1.4.0 > [4] RCurl_0.97-3 > [5] bitops_1.0-4.1 > [6] org.Hs.eg.db_2.2.11 > [7] microRNA_1.2.0 > [8] Rlibstree_0.3-2 > [9] Biostrings_2.12.4 > [10] IRanges_1.2.2 > [11] genefilter_1.24.2 > [12] humanStemCell_0.2.0 > [13] hgu133plus2.db_2.2.11 > [14] RSQLite_0.7-1 > [15] DBI_0.2-4 > [16] AnnotationDbi_1.6.0 > [17] affy_1.22.0 > [18] Biobase_2.4.1 > [19] limma_2.18.1 > [20] biomaRt_2.0.0 > > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 preprocessCore_1.6.0 > [4] splines_2.9.0 survival_2.35-4 tools_2.9.0 > [7] XML_2.3-0 xtable_1.5-5 > > Best, > > Jim > > > > Michael Lawrence wrote: > > On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders at="" ebi.ac.uk=""> <mailto:anders at="" ebi.ac.uk="">> wrote: > > Hi Michael, > > I've just tried to use rtracklayer, following your vignette, > and ran into > two problems. > > > 1. I cannot add any tracks to a session. > > I entered the code in the vignette to produce the "targets" > track and > exported it as "targets.bed". To make things easier to > follow, let's say, I > start from there with a fresh R session: > > library(rtracklayer) > > # Import the data > targets <- import("targets.bed") > # targets is now a RangedData object with 3052 ranges and > # sequence names chr1 chr10 chr11 chr12 ... > > # Create a session > session <- browserSession("UCSC") > > # Add the 'targets' track to the session: > track(session, "MYTRACK") <- targets > > Is this last command correct? It does not produce an error, > but it does not > seem to do anything, either. If I list all the tracks in the > session with > trackNames(session) > I get a list of 196 UCSC standard tracks, but "MYTRACK" is > not mentioned. > > How do I correctly add a track? > > > Well, I can say that this works for me. I need to look into > parsing the > error messages returned by UCSC. You can always try uploading > to UCSC > manually to see what went wrong. I know that back in December > the BED output > was mishandling the score values. > > > > 2. There is some mangling happening with the chromosome names. > > The man page for 'browserView' suggests to try: > > browserView(session, GenomicRanges(20000, 50000, "chr2")) > > Doing this asks my web browser to open the following URL: > > > http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 > <http: genome.ucsc.edu="" cgi-="" bin="" hgtracks?position="chrchr2%3a20000-50000&amp;hgsid=133834314"> > > Note that it says "chrchr2", i.e., a superfluous "chr" got > prefixed to the > sequence name. Obviously, the UCSC page cannot deal with > this and one gets > an error message displayed by JavaScript that "chrchr2" is > not known. > > I run into the same problem if I follow the vignette's code > to demonstrate > 'browserView'. > > If I try > browserView(session, GenomicRanges(20000, 50000, "2")) > I get the range chr2:20000-50000 correctly displayed in my > web browser. > There is, however, still now sight of "MYTRACK". > > What's going wrong here? > > > Thanks for pointing this out. I've fixed this for version 1.5.3. > > Michael > > > > sessionInfo() > > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC _COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en _GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.U TF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] rtracklayer_1.4.0 RCurl_0.94-1 > > loaded via a namespace (and not attached): > [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 > IRanges_1.2.0 > [5] XML_2.3-0 > > > Cheers > Simon > > > +--- > | Dr. Simon Anders, Dipl. Phys. > | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK > | office phone +44-1223-492680, mobile phone +44-7505-841692 > | preferred (permanent) e-mail: sanders at fs.tum.de > <mailto:sanders at="" fs.tum.de=""> > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLY
0
Entering edit mode
Maybe Jim and Simon have something different with their network configuration, e.g. routing through a proxy, or something. Michael On Fri, Jun 5, 2009 at 5:57 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Michael Lawrence wrote: > > >> >> On Thu, Jun 4, 2009 at 7:03 AM, James W. MacDonald <jmacdon@med.umich.edu<mailto:>> jmacdon@med.umich.edu>> wrote: >> >> Hi Michael, >> >> I get the same results as Simon. In fact, if I source() the vignette >> code and then run some of the chunks that are set to eval=false, I >> get errors: >> >> > source("c:/R-2.9.0/library/rtracklayer/doc/rtracklayer.R") >> Loading required package: hgu133plus2.db >> Loading required package: AnnotationDbi >> Loading required package: DBI >> Loading required package: Biostrings >> Loading required package: IRanges >> [snip] >> >> > session <- browserSession("UCSC") >> > track(session, "targets") <- targetTrack >> > targetTrack >> RangedData: 3063 ranges by 3 columns >> columns(3): strand name target >> sequences(23): chr1 chr10 chr11 chr12 chr13 ... chr7 chr8 chr9 chrX >> > view <- browserView(session, range(targetTrack)*-10, pack="targets") >> Error in validObject(x) : >> invalid class "IRanges" object: the widths must be non-NA integers >> In addition: Warning message: >> In numeric2integer(value) : NAs introduced by coercion >> Error in ucscForm(range) : >> error in evaluating the argument 'object' in selecting a method for >> function 'ucscForm' >> > view <- browserView(session, range(subTargetTrack) * -10,pack = >> "targets") >> Error in resolveTrackIndex(x, i) : Unknown tracks:targets >> >> If I export targetTrack as a bedfile and upload to UCSC I get no >> errors and can view the track without problems. >> >> >> I'm kind of at a loss here. I have your same sessionInfo on my machine >> (fresh R install, everything via biocLite) and yet it seems to work just >> fine. What's your curl version? Mine is 7.19.4. >> > > I am on Windows, and am using the binary from BioC, so the curl version is > whatever you guys are using to build the package with. I assume it is > relatively new? > > Jim > > > >> Michael >> >> >> On another subject, you might consider replacing the plot of the >> cpneTrack in the vignette with a .png rather than a .pdf. Trying to >> scroll through the vignette is a real drag when you get to that plot. >> >> >> Yes, good idea. >> >> >> >> > sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods >> [7] base >> >> other attached packages: >> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 >> [2] BSgenome_1.12.2 >> [3] rtracklayer_1.4.0 >> [4] RCurl_0.97-3 >> [5] bitops_1.0-4.1 >> [6] org.Hs.eg.db_2.2.11 >> [7] microRNA_1.2.0 >> [8] Rlibstree_0.3-2 >> [9] Biostrings_2.12.4 >> [10] IRanges_1.2.2 >> [11] genefilter_1.24.2 >> [12] humanStemCell_0.2.0 >> [13] hgu133plus2.db_2.2.11 >> [14] RSQLite_0.7-1 >> [15] DBI_0.2-4 >> [16] AnnotationDbi_1.6.0 >> [17] affy_1.22.0 >> [18] Biobase_2.4.1 >> [19] limma_2.18.1 >> [20] biomaRt_2.0.0 >> >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 annotate_1.22.0 preprocessCore_1.6.0 >> [4] splines_2.9.0 survival_2.35-4 tools_2.9.0 >> [7] XML_2.3-0 xtable_1.5-5 >> >> Best, >> >> Jim >> >> >> >> Michael Lawrence wrote: >> >> On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders@ebi.ac.uk>> <mailto:anders@ebi.ac.uk>> wrote: >> >> Hi Michael, >> >> I've just tried to use rtracklayer, following your vignette, >> and ran into >> two problems. >> >> >> 1. I cannot add any tracks to a session. >> >> I entered the code in the vignette to produce the "targets" >> track and >> exported it as "targets.bed". To make things easier to >> follow, let's say, I >> start from there with a fresh R session: >> >> library(rtracklayer) >> >> # Import the data >> targets <- import("targets.bed") >> # targets is now a RangedData object with 3052 ranges and >> # sequence names chr1 chr10 chr11 chr12 ... >> >> # Create a session >> session <- browserSession("UCSC") >> >> # Add the 'targets' track to the session: >> track(session, "MYTRACK") <- targets >> >> Is this last command correct? It does not produce an error, >> but it does not >> seem to do anything, either. If I list all the tracks in the >> session with >> trackNames(session) >> I get a list of 196 UCSC standard tracks, but "MYTRACK" is >> not mentioned. >> >> How do I correctly add a track? >> >> >> Well, I can say that this works for me. I need to look into >> parsing the >> error messages returned by UCSC. You can always try uploading >> to UCSC >> manually to see what went wrong. I know that back in December >> the BED output >> was mishandling the score values. >> >> >> >> 2. There is some mangling happening with the chromosome names. >> >> The man page for 'browserView' suggests to try: >> >> browserView(session, GenomicRanges(20000, 50000, "chr2")) >> >> Doing this asks my web browser to open the following URL: >> >> >> >> http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 >> < >> http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 >> > >> >> Note that it says "chrchr2", i.e., a superfluous "chr" got >> prefixed to the >> sequence name. Obviously, the UCSC page cannot deal with >> this and one gets >> an error message displayed by JavaScript that "chrchr2" is >> not known. >> >> I run into the same problem if I follow the vignette's code >> to demonstrate >> 'browserView'. >> >> If I try >> browserView(session, GenomicRanges(20000, 50000, "2")) >> I get the range chr2:20000-50000 correctly displayed in my >> web browser. >> There is, however, still now sight of "MYTRACK". >> >> What's going wrong here? >> >> >> Thanks for pointing this out. I've fixed this for version 1.5.3. >> >> Michael >> >> >> >> sessionInfo() >> >> R version 2.9.0 (2009-04-17) >> x86_64-unknown-linux-gnu >> >> locale: >> >> >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=e n_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID ENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] rtracklayer_1.4.0 RCurl_0.94-1 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 >> IRanges_1.2.0 >> [5] XML_2.3-0 >> >> >> Cheers >> Simon >> >> >> +--- >> | Dr. Simon Anders, Dipl. Phys. >> | European Bioinformatics Institute, Hinxton, Cambridgeshire, >> UK >> | office phone +44-1223-492680, mobile phone +44-7505-841692 >> | preferred (permanent) e-mail: sanders@fs.tum.de >> <mailto:sanders@fs.tum.de> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
On Thu, Jun 4, 2009 at 7:03 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Michael, > > I get the same results as Simon. In fact, if I source() the vignette code > and then run some of the chunks that are set to eval=false, I get errors: > > > source("c:/R-2.9.0/library/rtracklayer/doc/rtracklayer.R") > Loading required package: hgu133plus2.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: Biostrings > Loading required package: IRanges > [snip] > > > session <- browserSession("UCSC") > > track(session, "targets") <- targetTrack > > targetTrack > RangedData: 3063 ranges by 3 columns > columns(3): strand name target > sequences(23): chr1 chr10 chr11 chr12 chr13 ... chr7 chr8 chr9 chrX > > view <- browserView(session, range(targetTrack)*-10, pack="targets") > Error in validObject(x) : > invalid class "IRanges" object: the widths must be non-NA integers > In addition: Warning message: > In numeric2integer(value) : NAs introduced by coercion > Error in ucscForm(range) : > error in evaluating the argument 'object' in selecting a method for > function 'ucscForm' I guess I was just focusing on the missing track. Thinking about this overflow problem, this line does not even exist in the vignette, and it would cause a crash, since multiplying the maximum end of the entire track (on the order of a chromosome length) by 10 would overflow. > > view <- browserView(session, range(subTargetTrack) * -10,pack = > "targets") > Error in resolveTrackIndex(x, i) : Unknown tracks:targets > > If I export targetTrack as a bedfile and upload to UCSC I get no errors and > can view the track without problems. > > On another subject, you might consider replacing the plot of the cpneTrack > in the vignette with a .png rather than a .pdf. Trying to scroll through the > vignette is a real drag when you get to that plot. > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods > [7] base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 > [2] BSgenome_1.12.2 > [3] rtracklayer_1.4.0 > [4] RCurl_0.97-3 > [5] bitops_1.0-4.1 > [6] org.Hs.eg.db_2.2.11 > [7] microRNA_1.2.0 > [8] Rlibstree_0.3-2 > [9] Biostrings_2.12.4 > [10] IRanges_1.2.2 > [11] genefilter_1.24.2 > [12] humanStemCell_0.2.0 > [13] hgu133plus2.db_2.2.11 > [14] RSQLite_0.7-1 > [15] DBI_0.2-4 > [16] AnnotationDbi_1.6.0 > [17] affy_1.22.0 > [18] Biobase_2.4.1 > [19] limma_2.18.1 > [20] biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 preprocessCore_1.6.0 > [4] splines_2.9.0 survival_2.35-4 tools_2.9.0 > [7] XML_2.3-0 xtable_1.5-5 > > Best, > > Jim > > > > Michael Lawrence wrote: > >> On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders@ebi.ac.uk> wrote: >> >> Hi Michael, >>> >>> I've just tried to use rtracklayer, following your vignette, and ran into >>> two problems. >>> >>> >>> 1. I cannot add any tracks to a session. >>> >>> I entered the code in the vignette to produce the "targets" track and >>> exported it as "targets.bed". To make things easier to follow, let's say, >>> I >>> start from there with a fresh R session: >>> >>> library(rtracklayer) >>> >>> # Import the data >>> targets <- import("targets.bed") >>> # targets is now a RangedData object with 3052 ranges and >>> # sequence names chr1 chr10 chr11 chr12 ... >>> >>> # Create a session >>> session <- browserSession("UCSC") >>> >>> # Add the 'targets' track to the session: >>> track(session, "MYTRACK") <- targets >>> >>> Is this last command correct? It does not produce an error, but it does >>> not >>> seem to do anything, either. If I list all the tracks in the session with >>> trackNames(session) >>> I get a list of 196 UCSC standard tracks, but "MYTRACK" is not mentioned. >>> >>> How do I correctly add a track? >>> >>> >> Well, I can say that this works for me. I need to look into parsing the >> error messages returned by UCSC. You can always try uploading to UCSC >> manually to see what went wrong. I know that back in December the BED >> output >> was mishandling the score values. >> >> >> >>> 2. There is some mangling happening with the chromosome names. >>> >>> The man page for 'browserView' suggests to try: >>> >>> browserView(session, GenomicRanges(20000, 50000, "chr2")) >>> >>> Doing this asks my web browser to open the following URL: >>> >>> >>> >>> http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 >>> >>> Note that it says "chrchr2", i.e., a superfluous "chr" got prefixed to >>> the >>> sequence name. Obviously, the UCSC page cannot deal with this and one >>> gets >>> an error message displayed by JavaScript that "chrchr2" is not known. >>> >>> I run into the same problem if I follow the vignette's code to >>> demonstrate >>> 'browserView'. >>> >>> If I try >>> browserView(session, GenomicRanges(20000, 50000, "2")) >>> I get the range chr2:20000-50000 correctly displayed in my web browser. >>> There is, however, still now sight of "MYTRACK". >>> >>> What's going wrong here? >>> >>> >> Thanks for pointing this out. I've fixed this for version 1.5.3. >> >> Michael >> >> >> >>> sessionInfo() >>>> >>> R version 2.9.0 (2009-04-17) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> >>> >>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=e n_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID ENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] rtracklayer_1.4.0 RCurl_0.94-1 >>> >>> loaded via a namespace (and not attached): >>> [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0 >>> [5] XML_2.3-0 >>> >>> >>> Cheers >>> Simon >>> >>> >>> +--- >>> | Dr. Simon Anders, Dipl. Phys. >>> | European Bioinformatics Institute, Hinxton, Cambridgeshire, UK >>> | office phone +44-1223-492680, mobile phone +44-7505-841692 >>> | preferred (permanent) e-mail: sanders@fs.tum.de >>> >>> >>> >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > [[alternative HTML version deleted]]
ADD REPLY

Login before adding your answer.

Traffic: 341 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6