addGenomeData-gapSites {spliceSites} | R Documentation |
gapSites
object.The function takes an gapSites object, adds annotation data, MaxEnt-scores, Exon-Intron sequences to featureData slot.
object |
gapSites object |
dna |
DNAStringSet containing genomic sequence. |
junc |
refJunctions |
The function adds new columns to featureData
as described
in varMetadata
.
gapSites
Wolfgang Kaisers
# A) Read gapSites bam <- system.file("extdata", "rna_fem.bam", package="spliceSites") reader <- bamReader(bam, idx=TRUE) ga <- alignGapList(reader) bamClose(reader) # B) Load DNA dnafile <- system.file("extdata", "dna_small.RData", package="spliceSites") load(dnafile) # C) maxEnt mes<-load.maxEnt() gae<-addMaxEnt(ga,dna_small,mes) getMeStrand(gae) sae<-setMeStrand(gae) # D) Load annotation data ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites") juc <- loadGenome(ucf) esg <- addGenomeData(ga, dna_small, juc)