extractRange {spliceSites}R Documentation

extractRange: Extract subset from object where records lie in given range.

Description

Searches in object for data which lie inside the given range and returns an object of same type containing extracted data.

Usage

extractRange(object,seqid,start,end)

Arguments

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.

Value

Same type as object

Author(s)

Wolfgang Kaisers

Examples

# 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)
[Package spliceSites version 1.31.0 Index]