get_path_df: Get data.frame for plotting gene expression values of a...

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Get data.frame for plotting gene expression values of a pathway

Description

Get data.frame for plotting gene expression values of a pathway

Usage

get_path_df(top_table, path_id = NULL, pert_signature = NULL, nmax = 200)

Arguments

path_id	String with KEGG pathway id.
nmax	Maximum number of genes to keep from CMAP02/L1000 common and CMAP02 only genes for Drug and genetic query genes. Default is 200 so that all drug and genetic query genes are shown.
path_genes	Character vector of custom genes to construct pathway data.frame for.

Value

data.frame with columns:

• Gene gene names.

• Dprime standardized unbiased effect size values.

• sd standard deviations of Dprime.

• Link url to GeneCards page for gene.

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.