View source: R/expression_funks.R
transcriptsPerKilobaseMillion | R Documentation |
Calculates Reads Per Kilobase Million (RPKM) RPKM = (Rg * 10^9) / (T * Lg) where Rg: number of reads mapped to a particular transcript g = count T = total number of transcripts sampled in run Lg: length of transcript g (bases) Note, that because we use gene length in bases and not in kilobases the scaling factor is 10^9 and not 10^6.
transcriptsPerKilobaseMillion(raw.count.tbl, gene.col = "gene",
gene.length.col = "gene.length",
replicate.cols = setdiff(colnames(raw.count.tbl), c(gene.col,
gene.length.col)))
raw.count.tbl |
A data.frame with at least three columns: One must contain gene IDs (accessions), another the genes' lengths, and the other columns are expected to hold the read counts. |
gene.col |
The column name or number in which to find the gene identifier (accessions). Default is 'gene'. |
gene.length.col |
The column name or number in which to find the gene lengths. Default is 'gene.length'. |
replicate.cols |
The names or numbers of the columns in which to find
the raw read counts. Default is |
An extended version of raw.count.tbl
with added columns of
the RPKM values, one column for each column of raw reads in argument
replicate.cols
.
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