makeFinalOutput: Make Final Output

In ELELAB/lipidQ: Lipidomics Analysis Tool

Description

This function creates the final output file of the results which consists of both all filtered pmol species and filtered pmol classes.

Usage

makeFinalOutput(classPmol_molPctClass, pmolCalculatedDataSet,
  userSpecifiedColnames = NULL)

Arguments

classPmol_molPctClass	compact output file created by using the compactOutput_pmolCalc() script.
pmolCalculatedDataSet	data of pmol calculations made by using the pmolCalc() script.
userSpecifiedColnames	the column names template file containing user specified column names for the input data.

Value

a final output file containing pmol and mol

Author(s)

André Vidas Olsen

Examples

# load endo & ISTD databases as well as user specified column names file.
endogene_lipid_db <- read.table(system.file("extdata/dataTables/checks",
 "endogene_lipid_db.csv", package = "lipidQ"), stringsAsFactors = FALSE,
 header = TRUE, sep = ",")

ISTD_lipid_db <- read.table(system.file("extdata/dataTables/checks",
 "ISTD_lipid_db.csv", package = "lipidQ"), stringsAsFactors = FALSE,
 header = TRUE, sep = ",")

userSpecifiedColnames <- read.table(system.file("extdata/LipidQ_DataBase",
 "userSpecifiedColnames.csv", package = "lipidQ"),
 stringsAsFactors = FALSE, header = TRUE, sep = ",")

# load pmolCalculatedDataSet.csv made by using the pmolCalc() function
pmolCalculatedDataSet <- read.table(system.file("extdata/dataTables/checks",
 "pmolCalculatedDataSet.csv", package = "lipidQ"),
 stringsAsFactors = FALSE, header = TRUE, sep = ",")

# make compact output from pmolCalculatedDataSet
classPmol_molPctClass_compact <-
 compactOutput_pmolCalc(pmolCalculatedDataSet,
 userSpecifiedColnames = userSpecifiedColnames)

# make final outout
finalOutput <- makeFinalOutput(classPmol_molPctClass_compact,
 pmolCalculatedDataSet, userSpecifiedColnames = userSpecifiedColnames)

# print mol% final output
finalOutput[[1]]

# print pmol final output
finalOutput[[2]]

ELELAB/lipidQ documentation built on Feb. 24, 2020, 12:54 a.m.