imSigned2list_dep: convert signed incidence matrix to list

In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

convert signed incidence matrix to list

Description

convert signed incidence matrix to list

Usage

imSigned2list_dep(x, verbose = FALSE, ...)

Details

This function converts an signed incidence matrix that contains positive and negative values, or equivalent data.frame, to a list of named vectors containing values c(-1, 1) to indicate signed direction. The input matrix should contain numeric values where positive and negative values indicate directionality. When the input contains only logical values c(TRUE,FALSE) the direction is assumed to be +1 positive.

Values of NA are converted to zero 0 and therefore ignored.

This function uses the transactions class from the arules R package, which in our testing is substantially faster than similar techniques from a variety of other R packages.

Value

list of named numeric vectors, where list names are defined by colnames(x), and vector names are derived from rownames(x). Values in each vector indicate the signed direction, c(-1,1).

See Also

Other jam list functions: colors_from_list(), im2list_dep(), im2list(), imSigned2list(), list2concordance(), list2imSigned(), list2im()

jmw86069/jamenrich documentation built on Feb. 3, 2024, 12:40 p.m.