trim {spliceSites} | R Documentation |
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.
trim_left(x,maxlen)
x |
gapSites. Object from which the lJunc values are calculated. |
maxlen |
Numeric. Maximum number of nucleotides on feature (exon) side of boundary. |
None.
Wolfgang Kaisers
# 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