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

In wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.