patternMarkers {CoGAPS} | R Documentation |
patternMarkers
patternMarkers(Amatrix = NA, scaledPmatrix = FALSE, Pmatrix = NA, threshold = "all", lp = NA, full = FALSE)
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 |
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.