groupval-methods {xcms} | R Documentation

## Extract a matrix of peak values for each group

### 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`

[Package xcms version 3.0.2 Index]