dnaRanges {spliceSites} | R Documentation

## Reads a bamRange object for a given `bamReader`, `refGenome` and gene name.

### Description

Locates gene in genome via `refGenome` and reads a `bamRange` from the determined region.

### Usage

    dnaRanges(x,dnaset,useStrand=TRUE,removeUnknownStrand=TRUE,verbose=TRUE,...)

### Arguments

`x` | cRanges. Range-data will be copied from this object.
`dnaset` | DNAStringSet. Contains the reference sequence from which the DNA-sequence is extracted.
`useStrand` | logical. When TRUE, sequences for which strand='-' are reverse-complemented.
`removeUnknownStrand` | logical. When TRUE, sequences for which strand='-' are removed.
`verbose` | logical. Determines amount of console output during routine runtime.
`...` | Optional additional arguments (currently unused).

### Value

cdRanges

### Author(s)

Wolfgang Kaisers

### Examples

    bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
    reader<-bamReader(bam,idx=TRUE)
    ga<-alignGapList(reader)
    bamClose(reader)
    lj<-lJunc(ga,featlen=6,gaplen=6,strand='+')
    dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
    load(dnafile)
    ljd<-dnaRanges(lj,dna_small)
    seqlogo(ljd)

[Package spliceSites version 1.28.0 Index]