Created
August 22, 2011 06:07
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Convert feature counts into RPKM counts per gene
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| setGeneric("calcFPKMs", function(counts, ...) {standardGeneric("calcFPKMs")}) | |
| setMethod("calcFPKMs", c("GRanges"), | |
| function(counts, verbose = TRUE) | |
| { | |
| counts.df <- as.data.frame(counts) | |
| counts.cols <- metadata(counts)[["counts.cols"]] + 5 | |
| # Only use read counts from the known transcriptome. | |
| counts.df <- counts.df[counts.df[, "type"] %in% c("exon", "junction"), ] | |
| gene.id <- counts.df[, "gene"] | |
| gene.loc.expr <- by(counts.df, gene.id, function(x) | |
| { | |
| exons <- x[x[, "type"] == "exon", ] | |
| gene.start <- min(x[, "start"]) | |
| gene.end <- max(x[, "end"]) | |
| exonic.bases <- sum(exons[, "end"] - exons[, "start"]) | |
| list(c(gene.start, gene.end), | |
| colSums(x[, counts.cols]) / (exonic.bases / 1000) / (metadata(counts)[["totals"]] / 1000000)) | |
| }) | |
| genes.FPKMs <- do.call(rbind, lapply(gene.loc.expr, "[[", 2)) | |
| gene.locs <- do.call(rbind, lapply(gene.loc.expr, "[[", 1)) | |
| colnames(genes.FPKMs) <- paste(colnames(genes.FPKMs), "FPKM") | |
| gene.match <- match(rownames(genes.FPKMs), gene.id) | |
| gene.chr.strand <- counts.df[gene.match, c("seqnames", "strand")] | |
| result <- GRanges(gene.chr.strand[, "seqnames"], IRanges(gene.locs[, 1], gene.locs[, 2]), gene.chr.strand[, "strand"]) | |
| if("gene.symbol" %in% colnames(counts.df)) | |
| { | |
| values(result) <- DataFrame(gene = rownames(genes.FPKMs), gene.symbol = counts.df[gene.match, "gene.symbol"], genes.FPKMs) | |
| } else { | |
| values(result) <- DataFrame(gene = rownames(genes.FPKMs), genes.FPKMs) | |
| } | |
| result | |
| }) |
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