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 1.28.0 Index]