get_missing: Compute Missing Rates of Biological Samples and Pooled Plasma...

In MetProc: Separate Metabolites into Likely Measurement Artifacts and True Metabolites

Description

Computes two missing rates per metabolite: 1. Missing rate of biological samples and 2. Missing rate of pooled plasma samples. Requires a metabolomics data matrix from read.met function as well as the indicies of pooled plasma and biological samples from get_group. Returns a list with the two missing rates across all metabolites

Usage

get_missing(df, ppind, sampind)

Arguments

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.
ppind	The indices of the pooled plasma samples.
sampind	The indices of the biological samples.

Value

A list with the missing rates of the pooled plasma samples and biological samples for all metabolites in dataframe. The keys are:

ppmiss	The pooled plasma missing rate for each metabolite
sampmiss	The biological sample missing rate for each metabolite

See Also

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

Examples

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') 

#Get the missing rates of each category for all metabolites
missrate <- get_missing(metdata,grps[['pp']],grps[['sid']]) 

MetProc documentation built on May 2, 2019, 2:42 a.m.