addGenomeData-gapSites: Add MaxEnt-scores, Exon-Intron junction sequences score to...

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

Description

The function takes an gapSites object, adds annotation data, MaxEnt-scores, Exon-Intron sequences to featureData slot.

Arguments

object	gapSites object
dna	DNAStringSet containing genomic sequence.
junc	refJunctions

Details

The function adds new columns to featureData as described in varMetadata.

Value

gapSites

Author(s)

Wolfgang Kaisers

Examples

# 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)

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