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

In yclement/xcms: LC-MS and GC-MS Data Analysis

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

yclement/xcms documentation built on April 10, 2020, 12:08 a.m.