Extract a matrix of peak values for each group
groupval-methods.RdGenerate a matrix of peak values with rows for every group and
columns for every sample. The value included in the matrix can
be any of the columns from the xcmsSet peaks slot
matrix. Collisions where more than one peak from a single sample
are in the same group get resolved with one of several user-selectable
methods.
Methods
- object = "xcmsSet"
groupval(object, method = c("medret", "maxint"), value = "index", intensity = "into")
Arguments
- object
the
xcmsSetobject- method
conflict resolution method,
"medret"to use the peak closest to the median retention time or"maxint"to use the peak with the highest intensity- value
name of peak column to enter into returned matrix, or
"index"for index to the corresponding row in thepeaksslot matrix- intensity
if
method == "maxint", name of peak column to use for intensity
Value
A matrix with with rows for every group and columns for every
sample. Missing peaks have NA values.