easyRNASeq correction methods {easyRNASeq} | R Documentation |
Convert a count table obtained from the easyRNASeq function into an RPKM corrected count table.
## S4 method for signature 'matrix,ANY,vector,vector' RPKM( obj, from = c("exons", "features", "transcripts", "bestExons", "geneModels", "islands"), lib.size = numeric(1), feature.size = integer(1), simplify = TRUE, ... )
obj |
An object of class |
from |
Determine the kind of coverage to use, choice limited to: exons, features, transcripts, bestExons, geneModels or islands. |
lib.size |
Precise the library size. It should be a named numeric list, i.e. named after the sample names. |
feature.size |
Precise the feature (e.g. exons, genes) sizes. It should be a named numeric list, named after the feature names. |
simplify |
If set to TRUE, whenever a feature (exon, feature, ...) is duplicated in the count table, it is only returned once. |
... |
additional arguments. See details |
RPKM accepts two sets of arguments:
RNAseq,character the
... are additional arguments to be passed to the
readCounts
method.
matrix,named vectornormalize a count matrix by providing the feature sizes (e.g. gene sizes) as a named vector where the names match the row names of the count matrix and the lib sizes as a named vector where the names match the column names of the count matrix.
A matrix
containing RPKM corrected read counts.
Nicolas Delhomme
## Not run: ## get an RNAseq object rnaSeq <- easyRNASeq(filesDirectory= system.file( "extdata", package="RnaSeqTutorial"), pattern="[A,C,T,G]{6}\\.bam$", format="bam", readLength=36L, organism="Dmelanogaster", chr.sizes=as.list(seqlengths(Dmelanogaster)), annotationMethod="rda", annotationFile=system.file( "data", "gAnnot.rda", package="RnaSeqTutorial"), count="exons", outputFormat="RNAseq") ## get the RPKM rpkm <- RPKM(rnaSeq,from="exons") ## the same from a count table count.table <- readCounts(rnaSeq,count="exons") ## get the RPKM ## verify that the feature are sorted as the count.table all(.getName(rnaSeq,"exon") == rownames(count.table)) feature.size <- unlist(width(ranges(rnaSeq))) ## verify that the samples are ordered in the same way all(names(librarySize(rnaSeq)) == colnames(count.table)) ## get the RPKM rpkm <- RPKM(count.table, feature.size=feature.size, lib.size=librarySize(rnaSeq)) ## End(Not run)