trim {spliceSites} | R Documentation

## trim and resize methods: trim_left, trim_right, resize_left, resize_right

### Description

The trim and resize functions change number of nucleotides contained in align-gap features (exonic). Trim functions cut feature sizes down to `maxlen`. Resize functions reset all sizes to a fixed value. The functions operate directly on the passed objects. There is no return value.

### Usage

    trim_left(x,maxlen)

### Arguments

`x` | gapSites. Object from which the lJunc values are calculated.
`maxlen` | Numeric. Maximum number of nucleotides on feature (exon) side of boundary.

### Value

None.

### Author(s)

Wolfgang Kaisers

### Examples

    # A) Create gapSites object
    bam<-system.file("extdata","rna_fem.bam",package="spliceSites")
    reader<-bamReader(bam[1],idx=TRUE)
    ga<-alignGapList(reader)
    bamClose(reader)
    ga
    # B) Trim
    trim_left(ga,3)
    trim_right(ga,2)
    ga
    # C) Resize
    resize_left(ga,5)
    resize_right(ga,6)
    ga

[Package spliceSites version 1.28.0 Index]