uniqueJuncAnn: uniqueJuncAnn method for ExpressionSet

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

Description

uniqueJuncAnns adds annotation data to ExpressionSet and removes not-matching sites.

Usage

uniqueJuncAnn(object,junc,ann=TRUE,...)

Arguments

object	ExpressionSet. Object containing gap-site expression data.
junc	refJunctions. Object containing splice-junction sites.
ann	logical. Default: TRUE. When TRUE the unannotated sites are removed, otherwise the annotated sites are removed.
...	Unused.

Value

ExpresssionSet

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)
ucj<-getSpliceTable(uc)

# E) Extract unique annotated junction sites.
uja<-uniqueJuncAnn(es,ucj)

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