normExp: Normalized expression transformation

In CeTF: Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

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)

CeTF documentation built on Nov. 25, 2020, 2 a.m.