groupval-methods: Extract a matrix of peak values for each group

Description Arguments Value Methods See Also

Description

Generate 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.

Arguments

object

the xcmsSet object

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 the peaks slot 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.

Methods

object = "xcmsSet"

groupval(object, method = c("medret", "maxint"), value = "index", intensity = "into")

See Also

xcmsSet-class


xcms documentation built on May 18, 2019, 2 a.m.