format_MetabolomicData: Formatting of metabolomic data for MetaboAnalystR.

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

This function initializes objects that will hold the metabolite data, formats peak intensity data into one of the formats acceptable by MetaboAnalystR, and sets the metabolite data object.

Usage

format_MetabolomicData(mSetObj, Peak.list, Sample.df, Sample.data, tbl.id, ...)

## S3 method for class 'pktable'
format_MetabolomicData(mSetObj, Peak.list, Sample.df, Sample.data, tbl.id, ...)

## S3 method for class 'mass_all'
format_MetabolomicData(mSetObj, Peak.list, Sample.df, Sample.data, tbl.id, ...)

## Default S3 method:
format_MetabolomicData(mSetObj, Peak.list, Sample.df, Sample.data, tbl.id, ...)

Arguments

mSetObj	NULL
Peak.list	data frame containing combined ion mode peaklist with ion mode duplicates removed.
Sample.df	data frame with class info as columns. Must contain a separate row entry for each unique sex/class combination. Must contain the columns 'Sex','Class','n','Endogenous'.
Sample.data	data frame with phenotype data as columns and a row for each study sample. First column must be a unique sample identifier with the header 'CT-ID'. Phenotype columns may vary, but must include two columns called 'Plate Number' and 'Plate Position' for determining run order.
tbl.id	character Table name to draw from database. Default is NULL
...	Arguments to pass parameters to database functions

Value

mSetObj

Examples

library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)) {
file <- system.file("extdata","Sample_Class.txt", package = "LUMA") # is case sensitive on Linux
Sample.df <- read.table(file, header = TRUE, sep = "\t")
file2 <- system.file("extdata","Sample_Data.csv", package = "LUMA") # is case sensitive on Linux
Sample.data <- read.table(file2, header = TRUE, sep = ",")
Peak.list <- Peaklist_db$Peaklist_Normalized
class(mSetObj) <- "pktable"
new_mSetObj <- format_MetabolomicData(mSetObj = mSetObj, Peak.list =
Peak.list, Sample.df = Sample.df, Sample.data = Sample.data)
new_mSetObj$dataSet$orig.cls

class(mSetObj) <- "mass_all"
new_mSetObj <- format_MetabolomicData(mSetObj = mSetObj, Peak.list =
                                        Peak.list, Sample.df = Sample.df, Sample.data = Sample.data)
new_mSetObj$dataSet$orig.cls
}

USEPA/LUMA documentation built on Aug. 29, 2020, 1:40 p.m.