retcor-methods {xcms} | R Documentation |
Use ``well behaved'' peak groups to calculate retention time deviations for every time point of each sample. Use smoothed deviations to align retention times.
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 |
method |
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 |
An xcmsSet
object
retcor(object, missing = 1, extra = 1,
method = c("loess", "linear"), span = .2,
family = c("gaussian", "symmetric"),
plottype = c("none", "deviation", "mdevden"),
col = NULL, ty = NULL)