Align retention times across samples

These two methods use “well behaved” peak groups to calculate retention time deviations for every time point of each sample. Use smoothed deviations to align retention times.

Methods

object = "xcmsSet"

retcor(object, missing = 1, extra = 1, smooth = c("loess", "linear"), span = .2, family = c("gaussian", "symmetric"), plottype = c("none", "deviation", "mdevden"), col = NULL, ty = NULL)

Arguments

object

the xcmsSet object

missing

number of missing samples to allow in retention time correction groups

extra

number of extra peaks to allow in retention time correction correction groups

smooth

either "loess" for non-linear alignment or "linear" for linear alignment

span

degree of smoothing for local polynomial regression fitting

family

if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re-descending M estimator is used with Tukey's biweight function, allowing outlier removal

plottype

if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density

col

vector of colors for plotting each sample

ty

vector of line and point types for plotting each sample

Value

An xcmsSet object

See also

xcmsSet-class, loess retcor.obiwarp