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Prepare GMT functions

clue_prepare_funs.Rd

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