rangeByGeneName {spliceSites} | R Documentation |
bamReader
, refGenome
and gene name.Locates gene in genome via refGenome
and reads a bamRange
from the determined region.
rangeByGeneName(reader,genome,gene,complex=TRUE)
reader |
Object of class (rbamtools) |
genome |
Object of class (refgenome) |
gene |
Single gene name (character) |
complex |
Logical. Passed to 'bamRange' function. When TRUE, only aligns with nCigar>1 are counted. |
bamRange
Wolfgang Kaisers
bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ucf<-system.file("extdata","uc_small.RData",package="spliceSites") uc<-loadGenome(ucf) range<-rangeByGeneName(reader,uc,"WASH7P") size(range)