extractByGeneName {spliceSites} | R Documentation |
The function takes a 'cRanges' object (or derived) and searches inside of given 'refGenome' object for gene names. From identified gene-name matches genomic target regions can be defined for wich in turn the contained sites are extracted.
extractByGeneName(object,geneNames,src,...)
object |
gapSites or cRanges (or derived). Object inside which the data is searched for. |
geneNames |
Character. Vector of gene names for which data is to be extracted. |
src |
refGenome. Contains gene annotation (for conversion of gene-name to genomic coordinates). |
... |
(currently unused) |
The function internally calls 'extractByGeneName' on 'refGenome'. This function also prints out non matching gene names. On the result, the function calls 'getGenePositions' from which the genomic regions can be extracted. For each gene, data is extracted via 'extractRange' and the resulting objects are then concatenated.
Same type as object
Wolfgang Kaisers
# A) Read gapSites from BAM bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ga<-alignGapList(reader) bamClose(reader) # B) Load DNAStringSet dnafile<-system.file("extdata","dna_small.RData",package="spliceSites") load(dnafile) # C) load refGenome ucf<-system.file("extdata","uc_small.RData",package="spliceSites") uc<-loadGenome(ucf) # D) For cRanges lj<-lJunc(ga,featlen=6,gaplen=3,strand='+') ljw<-extractByGeneName(lj,geneNames="WASH7P",src=uc) # E) For cdRanges ljc<-lCodons(lj,frame=2) ljcd<-dnaRanges(ljc,dna_small) ljcdw<-extractByGeneName(ljcd,geneNames="WASH7P",src=uc) # F) For caRanges ljca<-translate(ljcd) ljcaw<-extractByGeneName(ljca,geneNames="WASH7P",src=uc) # G) For gapSites lrj<-lrJunc(ga,lfeatlen=6,rfeatlen=6,strand='+') lrjw<-extractByGeneName(lrj,geneNames="WASH7P",src=uc)