Arguments
plottype
if deviation plot retention time deviation
profStep
step size (in m/z) to use for profile generation from
the raw data files
center
the index of the sample all others will be aligned
to. If center==NULL, the sample with the most peaks is chosen as default.
col
vector of colors for plotting each sample
ty
vector of line and point types for plotting each sample
response
Responsiveness of warping. 0 will give a linear warp based
on start and end points. 100 will use all bijective anchors
distFunc
DistFunc function: cor (Pearson's R) or cor_opt (default,
calculate only 10% diagonal band of distance matrix, better
runtime), cov (covariance), prd (product), euc (Euclidean distance)
gapInit
Penalty for Gap opening, see below
gapExtend
Penalty for Gap enlargement, see below
factorDiag
Local weighting applied to diagonal moves in alignment.
factorGap
Local weighting applied to gap moves in alignment.
localAlignment
Local rather than global alignment
initPenalty
Penalty for initiating alignment (for local
alignment only) Default: 0