gsva_scores_dist: GSVA score density distribution plot

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

GSVA score density distribution plot

Description

Plots GSVA scores distribution across samples after performing GSVA algorithm on samples in a dataset (gene expression matrix) for the up-regulated and down-regulated gene-sets of a given gene expression signature.

Usage

gsva_scores_dist(expr_mat, sig_df)

Arguments

expr_mat	Normalised expression data set matrix comprising the expression levels of genes (rows) for each sample (columns) in a data set. Row names are gene symbols and column names are sample IDs / names. Gene expression matrices can contain normalised (logCPM transformed) RNASeq or microarray transcriptomic data.
sig_df	Gene expression signature for a specific pathway given as data frame with the first column named "gene" containing a list of genes that are the most differentially expressed when the given pathway is active, and the second column named "expression" containing their corresponding expression in the gene signature: -1 for down-regulated genes and 1 for up-regulated genes.

Value

A density plot displaying distribution of GSVA scores obtained for the samples using up-regulated and down-regulated gene-sets from the gene signature

Author(s)

Anisha Thind [e-mail]

Examples

## Not run: gsva_scores_dist(ER_dataset, ER_sig)

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