addGenomeData-ExpressionSet {spliceSites} | R Documentation |
ExpressionSet
object.The function takes an ExpressionSet object generated by
readExpSet
, annotates featureData
and adds MaxEnt-scores, Exon-Intron sequences
to featureData slot.
addGenomeData(object, dna, junc)
object |
ExpressionSet object generated by readExpSet. |
dna |
DNAStringSet containing genomic sequence. |
junc |
refJunctions |
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.
ExpressionSet
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) 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)