foldChange: foldChange

In mjhelf/Metaboseek: Metaboseek platform

foldChange

Description

calculate fold changes between grouped columns of a matrix

Usage

foldChange(
  mx,
  groups,
  ctrl = NULL,
  calc = "mean",
  topgroup = T,
  maxFold = T,
  foldMaxK = 2,
  foldmode = "simple"
)

Arguments

mx	a matrix of positive numeric (intensity) values
groups	named list of intensity columns listed by group (as supplied by $anagroupnames or $anagroupnames_norm of MseekFT objects)
ctrl	character() naming the control group
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 (not recommended nor documented)

Details

GX in the following table means that this column is generated for each group in groups, with the group name as prefix. Columns in the returned data.frame:

• maxint maximum intensity value across all samples

• topgroup the group that has the highes mean intensity

• maxfold maximum fold change between any two group mean intensities

• maxfoldoverK (where K is an integer) fold change of Max intensity over kth largest intensity across all samples

• GX__minInt minimum intensity value within a group

• GX__meanInt mean intensity value within a group

• GX__foldOverRest fold change of mean of intensity values in this group over mean of intensities in all other groups

• GX__minFold fold change of MINIMUM intensity value in this group over MAXIMUM intensity value across all other samples outside of this group

• GX__minFoldMean fold change of MEAN intensity value in this group over MAXIMUM intensity value across all other samples outside of this group

• GX__foldOverCtrl fold change of mean of intensity values in this group over mean of intensities in control group

• GX__minFoldOverCtrl fold change of MINIMUM intensity value in this group over MAXIMUM intensity value in control group

• best_minFold Highest minFold value found across all groups

• best_minFoldMean Highest minFoldMean value found across all groups

• best_minFoldCtrl Highest minFoldOverCtrl value found across all groups

Value

data.frame with columns representing fold change information for data in mx, see Details

mjhelf/Metaboseek documentation built on April 23, 2022, 12:09 p.m.