patternMarkers {CoGAPS} | R Documentation |
calculate the most associated pattern for each gene
patternMarkers(object, threshold = "all", lp = NA, axis = 1) ## S4 method for signature 'CogapsResult' patternMarkers(object, threshold = "all", lp = NA, axis = 1)
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) |
By default a non-overlapping list of genes associated with each
lp
.
data(GIST) pm <- patternMarkers(GIST.result)