check_signature_vs_dataset: Validity check in gene signatures and gene expression...

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

Validity check in gene signatures and gene expression datasets

Description

This function performs a validity check against the gene signature and gene expression data set and filters genes that are absent in expression data set and /or are not expressed in at least 10% of the total number of samples. A bar plot of mean-normalised counts for each gene is also displayed.

Usage

check_signature_vs_dataset(norm_data, sig_df, barplot = TRUE)

Arguments

norm_data	Normalized gene expression data matrix
sig_df	A signature data frame containing two columns: the first column contains a list of gene (represented by gene symbols) that are differentially expressed in a given pathway and their relative expression values are given in the second column, with 1 representing up-regulated genes and -1 representing down-regulated genes.
barplot	optional Boolean parameter to display bar plot of mean-normalised gene counts following pre-processing performed by the function (default=TRUE).

Value

A filtered gene expression data matrix with gene symbols as row names and sample names / IDs as column names

Author(s)

Yi-Hsuan Lee [e-mail]

Examples

## Not run: check_signature_vs_dataset(norm_data, sig_df)

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