annotate-ExpressionSet: Adds annotation data to existing ExpressionSet (created by...

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

Description

Reads featureData from incoming Expression set which should contain range data on embedding exons for gap-sites. The annotate function then overlaps the ranges with given annotation data. The result of overlapping is written into a AnnotatedDataFrame.

Arguments

object	ExpressionSet
genome	refGenome

Value

AnnotatedDataFrame

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) Annotate ExpressionSet
ucf <- system.file("extdata", "uc_small.RData", package="spliceSites")
uc <- loadGenome(ucf)
juc <- getSpliceTable(uc)
ann <- annotate(es, juc)

wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.