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Read up/down drug signatures from a gene set library

Source: R/09_downstream.R
mx_read_signatures.Rd

Parses a GMT file or an Enrichr gene set library text file and pairs sets named "<drug> up" and "<drug> down" (case-insensitive, separated by a space, underscore or hyphen) into signatures for mx_drug_connectivity. Works with Enrichr's LINCS_L1000_Chem_Pert_Consensus_Sigs library.

Usage

mx_read_signatures(path)

Arguments

path

Path to a GMT or Enrichr library file (tab-separated: set name, description, genes...).

Value

A named list; each element is a list with character vectors up and down. Drugs lacking either direction are dropped.

See also

mx_drug_connectivity

Examples

f <- tempfile(fileext = ".gmt")
writeLines(c("drugA up\t\tG1\tG2\tG3", "drugA down\t\tG4\tG5"), f)
mx_read_signatures(f)
#> $drugA
#> $drugA$up
#> [1] "G1" "G2" "G3"
#> 
#> $drugA$down
#> [1] "G4" "G5"
#> 
#>