calc_dist: Comparison between gene deregulation and cell type...

In bcm-uga/RiTMIC: A R package for RegulatIon of Tumor MIcroenvironment Composition

Comparison between gene deregulation and cell type proportion.

Description

calc_dist groups samples according to their deregulation status for a given gene. It then computes for each cell type different metrics to evaluate the distance between the two groups of cell proportions. An important distance suggests a link between the gene expression and the cell type proportion.
Metrics:

Metric	Tested parameter	Computed parameter
Kantorovich distance	Transportation	Distance
Student's t-test	Mean comparison	-log10(p-value)
Kolmogorov-Smirnov test	Distribution comparison	-log10(p-value)

Usage

calc_dist(binary_penda, A)

Arguments

binary_penda	The binary matrix of deregulation 0/1 for each gene and each sample, can be obtain with the pre_treat function. Dimension n (genes) * p (samples).
A	The matrix of cell type proportions for each sample. Dimension p (samples) * k (cell types).

Value

A data frame with for each gene and each cell type the results of the 3 metrics.

bcm-uga/RiTMIC documentation built on June 16, 2022, 2:41 p.m.