patternMarkers {CoGAPS}R Documentation

patternMarkers

Description

patternMarkers

Usage

patternMarkers(Amatrix = NA, scaledPmatrix = FALSE, Pmatrix = NA,
  threshold = "all", lp = NA, full = FALSE)

Arguments

Amatrix

A matrix of genes by weights resulting from CoGAPS or other NMF decomposition

scaledPmatrix

logical indicating whether the corresponding pattern matrix was fixed to have max 1 during decomposition

Pmatrix

the corresponding Pmatrix (patterns X samples) for the provided Amatrix (genes x patterns). This must be supplied if scaledPmatrix is FALSE.

threshold

# the type of threshold to be used. The default "all" will distribute genes into pattern with the lowest ranking. The "cut" thresholding by the first gene to have a lower ranking, i.e. better fit to, a pattern.

lp

a vector of weights for each pattern to be used for finding markers. If NA markers for each pattern of the A matrix will be used.

full

logical indicating whether to return the ranks of each gene for each pattern

Value

By default a non-overlapping list of genes associated with each lp. If full=TRUE a data.frame of genes rankings with a column for each lp will also be returned.


[Package CoGAPS version 3.0.2 Index]