normExp: Normalized expression transformation

In cbiagii/pcitRif: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Normalized expression transformation

Description

Normalize the expression data of any type of experiment by columns, applying log(x + 1)/log(2).

Usage

normExp(tab)

Arguments

tab	A matrix or dataframe of expression data (i.e. TPM, counts, FPKM).

Value

Returns a table with normalized values.

Examples

# loading a simulated counts data
data('simCounts')

# getting the TPM matrix from counts
tpm <- apply(simCounts, 2, function(x) {
            (1e+06 * x)/sum(x)
            })

# normalizing TPM data
norm <- normExp(tpm)

cbiagii/pcitRif documentation built on Feb. 5, 2023, 9:03 p.m.