norm_factor: Calculate normalisation factor

In wanchanglin/rnaseqdea: RNA-Seq Differential Expression Analysis (rnaseqdea)

Calculate normalisation factor

Description

Calculate normalisation factor

Usage

norm_factor(
  data,
  method = c("DESeq", "TMM", "RLE", "UQ", "none"),
  norm.data = FALSE
)

Arguments

data	a data frame with gene x replicate format
method	differential analysis method
norm.data	a logical indicating whether normalise data or not

Value

a list with normalisation factor and normalised data if norm.data is TRUE otherwise an vector of normalisation factor

Examples

## data set from R package 'pasilla' 
dn <- system.file("extdata/pasilla_gene_counts.tsv", package = "rnaseqdea")
data <- read.table(dn, header = TRUE, row.names = 1, quote = "", comment.char = "")
keep <- rowSums(data) > 6000
data <- data[keep, ]
res <- norm_factor(data, norm.data = TRUE)
res$nf
head(res$norm.data)

wanchanglin/rnaseqdea documentation built on June 2, 2025, 1:05 a.m.