Normalise a raw count matrix using matched gene lengths. Gene lengths are aligned by gene identifier before calculating reads per kilobase and scaling each sample to one million TPM.
Arguments
- counts
Count matrix containing raw counts.
- featureLength
Effective length of genes generated from
getEffLen().
Value
df numeric. This function returns a dataframe of TPM normalized counts and final column containing feature length.
Examples
if (FALSE) { # \dontrun{
## Effective length of the gene
gene_info <- data.frame(GeneID = c("gene1", "gene2", "gene3"), Length = c(1000, 1500, 2000))
count_matrix <- matrix(c(10, 20, 30, 40, 50, 60),
nrow = 3, ncol = 2,
dimnames = list(c("gene2", "gene1", "gene3"), c("sample1", "sample2"))
)
test <- easyTPM(count_matrix, gene_info)
} # }