Title — c_do_adjustRtime_peakGroups • cXCMS

Title

Usage

c_do_adjustRtime_peakGroups(
  peaks,
  peakIndex,
  rtime,
  minFraction = 0.9,
  extraPeaks = 1,
  smooth = c("loess", "linear"),
  span = 0.2,
  family = c("gaussian", "symmetric"),
  peakGroupsMatrix = matrix(ncol = 0, nrow = 0),
  subset = integer(),
  subsetAdjust = c("average", "previous")
)

Arguments

peaks: The identified peaks and their positions
peakIndex: index of peak
rtime: retention times of samples
minFraction: the minimum number of samples a feature has to exist in to qualify as an "aligning feature"
extraPeaks: How many extra peaks are allowed in the area of alignment (can be high for large datasets with high drift)
smooth: smoothing of alignment
span: how many features should the non-linear alignment model look at simultaniously? close to 0 models highly non-linear drift and close to 1 models linear drift
family: kind of model
peakGroupsMatrix: the groups (used for minFraction)
subset: The code is rewritten such that the subset option is no longer available. All samples will be aligned.
subsetAdjust: see "subset"

Value

adjusted rtimes