clue_prepare_funs: Prepare GMT functions

In labsyspharm/cluequery: Query the Clue Database of Perturbations Using R

Prepare GMT functions

Description

Prepare GMT functions

Usage

clue_gmt_from_deseq2(result_df, name, alpha = 0.05)

clue_gmt_from_df(gene_set_df, drop_invalid = FALSE)

clue_gmt_from_list(up, down, name, drop_invalid = FALSE)

Arguments

result_df	Data frame returned by results function
name	Name of gene set.
alpha	Significance cutoff set during DESeq2 analysis.
gene_set_df	Data frame of gene sets. See Details for format.
drop_invalid	If TRUE, drop invalid gene sets with warning. Otherwise an error is raised.
up, down	Vectors of up- and down-regulated gene IDs.

Value

Named vector with paths to the GMT files for the up-regulated and the down-regulated gene sets.

Functions

• clue_gmt_from_deseq2: Prepare a DESeq2 result for Clue

• clue_gmt_from_df: Prepare gmt files from a data frame

• clue_gmt_from_list: Prepare gmt files from a list of genes

labsyspharm/cluequery documentation built on May 23, 2022, 6:25 a.m.