plot_sexcheck: Explore metadata by gene expression on the sex chromosomes.

In Sage-Bionetworks/sageseqr: Identify differentially expressed genes counts data

Explore metadata by gene expression on the sex chromosomes.

Description

This function plots expression of X and Y marker genes, XIST and UTY respectively, and colors each sample by the sex- or gender-specific labeling from the metadata. This is a handy check to determine if samples were swapped or mislabeled.

Usage

plot_sexcheck(clean_metadata, count_df, biomart_results, sex_var)

Arguments

clean_metadata	A data frame with sample identifiers as rownames and variables as factors or numeric as determined by "sageseqr::clean_covariates()".
count_df	A counts data frame with sample identifiers as column names and gene Ids are rownames.
biomart_results	Output of "sageseqr::get_biomart()". Gene Ids are stored as rownames.
sex_var	Column name of the sex or gender-specific metadata.

Sage-Bionetworks/sageseqr documentation built on June 13, 2024, 2:11 p.m.