uniqueJuncAnn {spliceSites} | R Documentation |
uniqueJuncAnns adds annotation data to ExpressionSet and removes not-matching sites.
uniqueJuncAnn(object,junc,ann=TRUE,...)
object |
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junc |
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ann |
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... |
Unused. |
ExpresssionSet
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) ucj<-getSpliceTable(uc) # E) Extract unique annotated junction sites. uja<-uniqueJuncAnn(es,ucj)