| foldChange {Mosaic} | R Documentation |
calculate fold changes between grouped columns of a matrix
foldChange(mx, groups, ctrl = NULL, calc = "mean", topgroup = T, maxFold = T, foldMaxK = 2, foldmode = "simple")
mx |
a matrix of numeric (intensity) values |
groups |
named list of intensity columns listed by group (as supplied by $anagroupnames or $anagroupnames_norm of MosaicFT objects) |
ctrl |
character() naming the control group(s) |
calc |
currently has to be "mean", compare rowMeans of one group vs. rowMeans of other groups (and optionally rowMeans of controls only) |
topgroup |
if TRUE, return group with highest intensity for each feature |
maxFold |
if TRUE, make a column with maximum fold change between any two groups for each feature |
foldMaxK |
if not NULL, make column with fold change of highest group value over foldMaxK largest group value. |
foldmode |
if "complex", gives ratios between all groups |