getGapSites {spliceSites} | R Documentation |
gapSites
getGapSites
and alignGapList
read gap-site data from single BAM-files (given as bamReader
) and return a gapSites
object. getGapSites
reads data for one seqid (given as 1-based numeric value). alignGapList
reads the whole BAM-file. The functions test for opened reader and initialized index.
getGapSites(reader,seqid,startid=1)
reader |
bamReader (rbamtools). An opened instance of |
seqid |
Numeric. 1-based index of reference sequence for which gap-sites are to be read. |
startid |
Numeric. Default: 1. Determines start value for |
getGapSites
internally calls rbamtools::gapList
. alignGapList
internally calls rbamtools::bamGapList
. 'nProbes' values are set to 1.
gapSites
Wolfgang Kaisers
bam<-system.file("extdata", "rna_fem.bam", package="spliceSites") reader<-bamReader(bam,idx=TRUE) gal<-getGapSites(reader,1,startid=10) gal gal<-alignGapList(reader) gal