get_group: Retrieve Index of Biological Samples and Pooled Plasma...
In MetProc: Separate Metabolites into Likely Measurement Artifacts and True Metabolites

Description Usage Arguments Value See Also Examples

View source: R/functions_cleane.R

Takes a metabolomics data matrix and retrieves the column indices of biological samples and pooled plasma samples. Columns must be ordered by injection order and each column ID should have a unique prefix designating the particular type of sample it is. For example, “PPP”' to designate pooled plasma samples and “X” to designate biological samples. Generally if data is read into R using the read.met function, columns will be labeled appropriately.

1	get_group(df, ppkey = "PPP", sidkey = "X")

`df`	The metabolomics dataset, ideally read from the `read.met` function. Each column represents a sample and each row represents a metabolite. Columns should be labeled with some unique prefix denoting whether the column is from a biological sample or pooled plasma sample. For example, all pooled plasma samples may have columns identified by the prefix “PPP” and all biological samples may have columns identified by the prefix “X”. Missing data must be coded as NA. Columns must be ordered by injection order.
`ppkey`	The unique prefix of pooled plasma samples. Default is `"PPP"`.
`sidkey`	The unique prefix of biological samples. Default is `"X"`.

A list of length 2 with the following keys:

`pp`	A vector with column indices of pooled plasma
`sid`	A vector with column indices of samples

See MetProc-package for examples of running the full process.

library(MetProc)
#Read metabolomics data
metdata <- read.met(system.file("extdata/sampledata.csv", package="MetProc"),
headrow=3, metidcol=1, fvalue=8, sep=",", ppkey="PPP", ippkey="BPP")

#Get groups based on samples and pooled plasma
grps <- get_group(metdata,'PPP','X')