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Question: RMAPPER and whole genome TFBS information
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gravatar for Ravi Karra
6.9 years ago by
Ravi Karra140
Ravi Karra140 wrote:
Hello, I am trying to identify all putative GATA binding sites in the mouse genome. Ideally, I want to get genomic coordinates for each "binding site" to enter into a GenomicRanges object (I know there will be a lot of hits) and to overlay this information with the results of a ChIP- Seq experiment. Seems that there are multiple packages to try and do this with, but only RMAPPER allows an interface with the TRANSFAC and Jaspar TF binding site models. I have been getting multiple errors that I am not sure how to resolve. Is this package the best way to get the information I want? Is there a better alternative? Is there an upper limit to the MAPPER query? Thanks for your help, Ravi #load the necessary libraries library (RMAPPER) library (biomaRt) #Compute the mouse genome #get identifiers to be input into MAPPER mm = useMart (biomart = "ensembl", dataset = "mmusculus_gene_ensembl") mmGenes = getBM (attributes = c ("ensembl_gene_id", "external_gene_id", "entrezgene", "external_transcript_id"), mart = mm) #get list of all entrez gene id's egids = unique (mmGenes$entrezgene); egids = egids [2:length (egids)] #first id is NA #make a list of all geneids eglist = paste (egids [500:550], collapse = ",") #get the factor models gata = "M00789, T02689, T00311, T00306, T00305, T00267, T00305, T00267, T00306, T00311, M00632, M00462, MA0037" #Run MAPPER with 50 genes gatah = readMAPPER (gene = eglist, models = gata, org = "Mm", pbases = 5000) >Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open: HTTP status was '0 (null)' #Run MAPPER with 10 genes eglist = paste (egids [500:510], collapse = ",") gatah = readMAPPER (gene = eglist, models = gata, org = "Mm", pbases = 5000) > Error in seq.default(1, nh * 4, 4) : wrong sign in 'by' argument > traceback () 10: stop("wrong sign in 'by' argument") 9: seq.default(1, nh * 4, 4) 8: seq(1, nh * 4, 4) 7: `[.data.frame`(df, seq(1, nh * 4, 4), ) 6: df[seq(1, nh * 4, 4), ] 5: reshapeMapper(tmp) 4: initialize(value, ...) 3: initialize(value, ...) 2: new("mapperHits", query = sett, hits = reshapeMapper(tmp)) 1: readMAPPER(gene = eglist, models = gata, org = "Mm", pbases = 5000) > sessionInfo () R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.8.0 RMAPPER_1.2.0 loaded via a namespace (and not attached): [1] RCurl_1.5-0 tools_2.13.0 XML_3.2-0 [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.9 years ago by Vincent J. Carey, Jr.6.2k • written 6.9 years ago by Ravi Karra140
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gravatar for Vincent J. Carey, Jr.
6.9 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
I am listed as the author of this package, and indeed some years ago I wrote the R code that interfaces to the XML-RPC of MAPPER database. I don't know exactly why you are seeing the error that you are seeing, and as far as I can tell your inputs meet the requirement of the rmapperHelp() server-generated documentation. I registered to use the database manually and created a query that it processed as Gene: Trp53rk (transformation related protein 53 regulating kinase) Gene ID: 76367 mRNA accession: NM_023815 Organism: Mus musculus Scanned region: chr2:166617267-166626993 (click to download) Models: JASPAR matrices, TRANSFAC matrices, M00789 This yielded over 2400 hits, for example: Gene GeneID Transcript Factor Name(s) Strand Chrom Start End Region Score E-value Trp53rk 76367 NM_023815 M00791 HNF3 + chr2 166,617,268 166,617,279 Promoter 4.6 14 Trp53rk 76367 NM_023815 MA0041 Foxd3 - chr2 166,617,269 166,617,279 Promoter 2.9 11 Trp53rk 76367 NM_023815 MA0047 Foxa2 - chr2 166,617,269 166,617,280 Promoter 3.9 4.3 with further details on first hit Trp53rk 76367 NM_023815 M00791 HNF3 + chr2 166,617,268 166,617,279 Promoter 4.6 14 Gene: Trp53rk Factor: HNF3 Position (abs): chr2:166,617,268-166,617,279 Gene ID: 76367 Model: M00791 Position (tx): -1999 to -1988 mRNA: NM_023815 Alignment: *->taaacaaAca.a<-* t+ acaaA+a + TGTACAAATAtT Position (cds): -2045 to -2034 ENSEMBL: ENSMUSG00000042 Score: 4.6 E-value: 14 Gene region: Promoter Strand: + Conserved: - in principle RMAPPER will return all such information. However when I try to pass the related query information to readMapper function, I get a success code but just a header back -- no hit data is returned. Specifically > readMAPPER(gene="Trp53rk", models="M00789",org = "Mm", pbases = 2000) Error in seq.default(1, nh * 4, 4) : wrong sign in 'by' argument Enter a frame number, or 0 to exit 1: readMAPPER(gene = "Trp53rk", models = "M00789", org = "Mm", pbases = 2000) 2: new("mapperHits", query = sett, hits = reshapeMapper(tmp)) 3: initialize(value, ...) 4: initialize(value, ...) 5: reshapeMapper(tmp) 6: df[seq(1, nh * 4, 4), ] 7: `[.data.frame`(df, seq(1, nh * 4, 4), ) 8: seq(1, nh * 4, 4) 9: seq.default(1, nh * 4, 4) So I suggest you contact the maintainers. I will carbon them on this note. R version 2.13.0 Patched (2011-04-14 r55443) Platform: x86_64-apple-darwin10.6.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] org.Mm.eg.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 [4] AnnotationDbi_1.13.21 Biobase_2.11.10 biomaRt_2.8.0 [7] RMAPPER_1.3.0 weaver_1.17.0 codetools_0.2-8 [10] digest_0.4.2 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0 On Sat, Apr 16, 2011 at 10:41 PM, Ravi Karra <ravi.karra at="" gmail.com=""> wrote: > Hello, > > I am trying to identify all putative GATA binding sites in the mouse genome. ?Ideally, I want to get genomic coordinates for each "binding site" to enter into a GenomicRanges object (I know there will be a lot of hits) and to overlay this information with the results of a ChIP- Seq experiment. Seems that there are multiple packages to try and do this with, but only RMAPPER allows an interface with the TRANSFAC and Jaspar TF binding site models. > I have been getting multiple errors that I am not sure how to resolve. ?Is this package the best way to get the information I want? ?Is there a better alternative? ?Is there an upper limit to the MAPPER query? > > Thanks for your help, > Ravi > > #load the necessary libraries > library (RMAPPER) > library (biomaRt) > > #Compute the mouse genome > #get identifiers to be input into MAPPER > mm = useMart (biomart = "ensembl", dataset = "mmusculus_gene_ensembl") > mmGenes = getBM (attributes = c ("ensembl_gene_id", "external_gene_id", "entrezgene", "external_transcript_id"), mart = mm) > #get list of all entrez gene id's > egids = unique (mmGenes$entrezgene); egids = egids [2:length (egids)] #first id is NA > > #make a list of all geneids > eglist = paste (egids [500:550], collapse = ",") > > #get the factor models > gata = "M00789, T02689, T00311, T00306, T00305, T00267, T00305, T00267, T00306, T00311, M00632, M00462, MA0037" > > #Run MAPPER with 50 genes > gatah = readMAPPER (gene = eglist, models = gata, org = "Mm", pbases = 5000) > >>Error in file(con, "r") : cannot open the connection > In addition: Warning message: > In file(con, "r") : cannot open: HTTP status was '0 (null)' > > #Run MAPPER with 10 genes > eglist = paste (egids [500:510], collapse = ",") > gatah = readMAPPER (gene = eglist, models = gata, org = "Mm", pbases = 5000) > >> Error in seq.default(1, nh * 4, 4) : wrong sign in 'by' argument > > >> traceback () > 10: stop("wrong sign in 'by' argument") > 9: seq.default(1, nh * 4, 4) > 8: seq(1, nh * 4, 4) > 7: `[.data.frame`(df, seq(1, nh * 4, 4), ) > 6: df[seq(1, nh * 4, 4), ] > 5: reshapeMapper(tmp) > 4: initialize(value, ...) > 3: initialize(value, ...) > 2: new("mapperHits", query = sett, hits = reshapeMapper(tmp)) > 1: readMAPPER(gene = eglist, models = gata, org = "Mm", pbases = 5000) > >> sessionInfo () > R version 2.13.0 (2011-04-13) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] biomaRt_2.8.0 RMAPPER_1.2.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 ?tools_2.13.0 XML_3.2-0 > > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >
ADD COMMENTlink written 6.9 years ago by Vincent J. Carey, Jr.6.2k
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