imSigned2list: convert signed incidence matrix to list

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

convert signed incidence matrix to list

Description

convert signed incidence matrix to list

Usage

imSigned2list(x, empty = c(NA, "", 0, FALSE), ...)

Arguments

x	matrix or equivalent object with colnames(x) indicating list set names, and rownames(x) indicating list contents.
empty	character vector of incidence matrix values that should be considered "empty" and therefore do not indicate the row in x is present for the given column in x. All other items are considered to be present, and are assigned direction based upon the value in that cell of x.
...	additional arguments are ignored.

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.

Values that are logical with TRUE and FALSE are converted to numeric before output.

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_dep(), list2concordance(), list2imSigned(), list2im()

Examples

im <- matrix(c(0,1,-1,1,1,NA,-1,0,1),
   ncol=3,
   nrow=3,
   dimnames=list(letters[1:3], LETTERS[1:3]))
print(im);
# matrix input
im2list(im);
imSigned2list(im);
imSigned2list(im != 0);

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.