patternMarkers: patternMarkers

In genesofeve/GWCoGAPS:

Description

patternMarkers

Usage

patternMarkers(Amatrix = AP$Amean, scaledPmatrix = FALSE, Pmatrix = NA,
  threshold = "cut", 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 "cut" will thresholding by the first gene to have a lower ranking, i.e. better fit to, a pattern. Alternatively, threshold="all" will return all of the genes in rank order for each 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.

Examples

## Not run: 
patternMarkers(Amatrix=AP$Amean,scaledPmatrix=FALSE,Pmatrix=NA,threshold="cut")

## End(Not run)

genesofeve/GWCoGAPS documentation built on May 17, 2019, 1:10 a.m.