addGenomeData-ExpressionSet: 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 ExpressionSet object generated by readExpSet, annotates featureData and adds MaxEnt-scores, Exon-Intron sequences to featureData slot.

Usage

    addGenomeData(object, dna, junc)

Arguments

object	ExpressionSet object generated by readExpSet.
dna	DNAStringSet containing genomic sequence.
junc	refJunctions

Details

The function adds new columns to featureData as described in varMetadata. The ljseq and rjseq columns contain exon-intron junction sequence (from xJunc, dnaRanges using featlen=3, gaplen=8). The ldin and rdin columns contain first intronic dinucleotides from left and right gap-site border.

Value

ExpressionSet

Author(s)

Wolfgang Kaisers

Examples

# A) Names of BAM-files
bam <- character(2)
bam[1] <- system.file("extdata", "rna_fem.bam", package="spliceSites")
bam[2] <- system.file("extdata", "rna_mal.bam", package="spliceSites")

# B) Experiment Profile
prof <- data.frame(gender=c("f", "m"))
meta <- data.frame(labelDescription=names(prof), row.names=names(prof))
pd <- new("AnnotatedDataFrame", data=prof, varMetadata=meta)

# C) Read ExpressionSet
es <- readExpSet(bam, phenoData=pd)

# D) Load annotation data
ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites")
juc <- loadGenome(ucf)

# E) Add Genome data
dnafile<-system.file("extdata","dna_small.RData",package="spliceSites")
load(dnafile)
esg <- addGenomeData(es, dna_small, juc)

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