plotQC_totalLipids: picomol Calculation

In ELELAB/lipidQ: Lipidomics Analysis Tool

Description

This function creates QC plots of MS1 intensity data

Usage

plotQC_totalLipids(data, userSpecifiedColnames = NULL, pathToOutput = "")

Arguments

data	data formatted by the use of the compactOutput_pmolCalc function from LipidQ.
userSpecifiedColnames	the column names template file containing user specified column names for the input data.
pathToOutput	the directory path to save the plots

Value

barplots of pmol for every lipid class as well as one barplot of the total amount of lipids for each sample

Author(s)

André Vidas Olsen

Examples

# load user specified column names
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)

# create QC plot of of total lipids
plotQC_totalLipids(data = classPmol_molPctClass_compact,
 userSpecifiedColnames = userSpecifiedColnames,
 pathToOutput = "")

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