trim: trim and resize methods: trim_left, trim_right, resize_left,...

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

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

spliceSites documentation built on May 6, 2019, 3:05 a.m.