extractRange {spliceSites} | R Documentation |
Searches in object for data which lie inside the given range and returns an object of same type containing extracted data.
extractRange(object,seqid,start,end)
object |
gapSites or cRanges (or derived). Object inside which the data is searched for. |
seqid |
character. Reference sequence identifier. |
start |
numeric. Start position of given range. |
end |
numeric. End position of given range. |
Same type as object
Wolfgang Kaisers
# A) Read gapSites bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ga<-alignGapList(reader) bamClose(reader) # B) Load refGenome ucf<-system.file("extdata","uc_small.RData",package="spliceSites") uc<-loadGenome(ucf) # C) For gapSites extractRange(ga,seqid="chr1",start=14000,end=30000) # D) For cRanges lj<-lJunc(ga,featlen=3,gaplen=6,strand='+') extractRange(lj,seqid="chr1",start=14000,end=30000)