log_cpm_transform: Log CPM transformation of RNA-seq raw count data by using log...

In a-thind/PathAnalyser: ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets

Log CPM transformation of RNA-seq raw count data by using log CPM

Description

Performs a logCPM transformation of RNA-seq raw count data using the counts per million (CPM) method from the edgeR library. In addition to the log CPM transformation, the function can also plot a boxplot as sanity check for logCPM transformation of the gene expression matrix. The first series of boxplots display the distribution of the raw counts for each sample in thousands, while the second series of boxplots show the distribution of the logCPM normalised gene expression matrix.

Usage

log_cpm_transform(dataset, boxplot = TRUE)

Arguments

dataset	An unnormalised gene expression matrix containing raw RNA-seq (integer) counts with gene symbols as row names and sample IDs as column names.
boxplot	Optional argument that is a boolean (TRUE or FALSE) indicating whether boxplots displaying before and after log CPM transformation should be displayed. (Default=TRUE)

Value

A logCPM transformed gene expression data matrix with gene symbols as row names and samples names / IDs as column names.

Author(s)

Rishabh Kaushik and Taniya Pal [e-mail], [e-mail]

Examples

## Not run: log_cpm_transform(data.matrix)

a-thind/PathAnalyser documentation built on May 6, 2022, 9:50 a.m.