get_emt_score: Calculates Epithelial Mesenchymal transition (EMT) score

In korkutlab/imogimap: What the Package Does (One Line, Title Case)

Calculates Epithelial Mesenchymal transition (EMT) score

Description

Calculates Epithelial Mesenchymal transition (EMT) score

Usage

get_emt_score(pdf)

Arguments

pdf	A numeric data frame or matrix with samples as columns and gene/proteins as rows.

Details

To calculate EMT score, gene expressions in EMT_gene_list are weighted by their sign factor to account for the direction of the effect on EMT (See EMT_gene_list for list of genes and their direction of effect). The EMT_score is defined as mean value of modified expressions. Scores are then mean-centered and normalized by standard deviation based on distribution of scores in all samples.

Value

a dataframe of EMT scores for each sample

Examples

get_emt_score(pdf=sample_mRNA_data)

korkutlab/imogimap documentation built on March 17, 2023, 8:22 a.m.