Error in solveUserSEW0 when using get.targets in TEQC
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@johanna-hasmats-2403
Last seen 7.3 years ago
Dear all, I am trying to load the exome bed file "2.1M_Human_Exome.bed" provided by NimbleGen (http://www.nimblegen.com/downloads/annotation/seqcap_exome/2.1M_Human _Exome _Annotation.zip) as a target by using get.targets in the TEQC package. However, I get this error message: Error in solveUserSEW0(start = start, end = end, width = width) : solving row 175279: range cannot be determined from the supplied arguments (too many NAs) and I cannot seem to come around it. Tried if conditions as well as na.omit/exclude but without results. > traceback() 4: .Call("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") 3: solveUserSEW0(start = start, end = end, width = width) 2: IRanges(start = dat[, startcol], end = dat[, endcol]) 1: get.targets("2.1M_Human_Exome.bed", chrcol = 1, startcol = 2, endcol = 3) > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TEQC_0.99.2 IRanges_1.8.9 loaded via a namespace (and not attached): [1] Biobase_2.10.0 tools_2.12.2 Could somebody help me out with this? Thanks in advance, Johanna ############################################################ Kindly ? Johanna Hasmats, M.Sc, PhD Student Division of Gene Technology, School of Biotechnology, KTH SciLifeLab Phone: +46(0)73 625 14 60 ? Postal address: Box 1031 171 21 Solna ? Delivery address: KISP (Karolinska Institutet Science Park) Tomtebodav?gen 23B 171 65 Solna Sweden
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@herve-pages-1542
Last seen 9 hours ago
Seattle, WA, United States
Hi Johanna, As you can see, line 175279 in the 2.1M_Human_Exome.bed file is different from the other lines: > read.delim("2.1M_Human_Exome.bed", as.is=TRUE, skip=175277, nrows=5, header=FALSE) V1 V2 V3 1 chrY 26179378 26179600 2 chrY 26179986 26180066 3 track name=tiled_region description=NimbleGen Tiled Regions NA NA 4 chr1 58924 59145 5 chr1 59087 59167 I think that this how tracks are separated in a BED file. I don't know the details of how the TEQC::get.targets() function should be used but it seems that it is currently unable to load a BED file that contains more than 1 track. You could still use the 'skip' and 'nrows' argument to load only the track you want though. For example, to load the first track: > aa <- get.targets("2.1M_Human_Exome.bed", chrcol = 1, startcol = 2, endcol = 3, nrows=175278) [1] "read 175278 (non-overlapping) target regions" But that requires that you have a way to find out the right values to use for 'skip' and 'nrows'. A more convenient way to achieve the same result is to load the file with the import() function defined in the rtracklayer package: > library(rtracklayer) > bb <- import("2.1M_Human_Exome.bed", format="bed") > bb RangedDataList of length 2 names(2): target_region tiled_region Then if you want the first track: > as(bb[[1L]], "RangedData") This will give you the same thing as 'aa'. Finally note that TEQC has not been released yet. It's in BioC devel (BioC 2.8) and you are using BioC release (BioC 2.7). This is very likely to bring you troubles. Cheers, H. On 03/03/2011 08:08 AM, Johanna Hasmats wrote: > Dear all, > > I am trying to load the exome bed file "2.1M_Human_Exome.bed" provided by > NimbleGen > (http://www.nimblegen.com/downloads/annotation/seqcap_exome/2.1M_Hum an_Exome > _Annotation.zip) as a target by using get.targets in the TEQC package. > > However, I get this error message: > > Error in solveUserSEW0(start = start, end = end, width = width) : > solving row 175279: range cannot be determined from the supplied arguments > (too many NAs) > > and I cannot seem to come around it. Tried if conditions as well as > na.omit/exclude but without results. > >> traceback() > 4: .Call("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") > 3: solveUserSEW0(start = start, end = end, width = width) > 2: IRanges(start = dat[, startcol], end = dat[, endcol]) > 1: get.targets("2.1M_Human_Exome.bed", chrcol = 1, startcol = 2, > endcol = 3) > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] TEQC_0.99.2 IRanges_1.8.9 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 tools_2.12.2 > > Could somebody help me out with this? > > Thanks in advance, > > Johanna > > > ############################################################ > Kindly > > Johanna Hasmats, M.Sc, PhD Student > Division of Gene Technology, School of Biotechnology, KTH > SciLifeLab > Phone: +46(0)73 625 14 60 > > Postal address: > Box 1031 > 171 21 Solna > > Delivery address: > KISP (Karolinska Institutet Science Park) > Tomtebodav?gen 23B > 171 65 Solna > Sweden > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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