annotate-ExpressionSet {spliceSites} | R Documentation |
readExpSet
)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.
object |
ExpressionSet |
genome |
refGenome |
AnnotatedDataFrame
Wolfgang Kaisers
# 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)