patternMarkers-methods: compute pattern markers statistic

In CoGAPS: Coordinated Gene Activity in Pattern Sets

Description

calculate the most associated pattern for each gene

Usage

patternMarkers(object, threshold = "all", lp = NA, axis = 1)

## S4 method for signature 'CogapsResult'
patternMarkers(object, threshold = "all", lp = NA, axis = 1)

Arguments

object	an object of type CogapsResult
threshold	the type of threshold to be used. The default "all" will distribute genes into pattern with the lowest ranking. The "cut" thresholds 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.
axis	either 1 or 2, specifying if pattern markers should be calculated using the rows of the data (1) or the columns of the data (2)

Value

By default a non-overlapping list of genes associated with each lp.

Examples

data(GIST)
pm <- patternMarkers(GIST.result)

Example output

CoGAPS documentation built on Nov. 8, 2020, 5:02 p.m.