plotQC_ISTD: picomol Calculation

In ELELAB/lipidQ: Lipidomics Analysis Tool

Description

This function creates QC plots of MS1 intensity data

Usage

plotQC_ISTD(data, endogene_lipid_db, ISTD_lipid_db,
  userSpecifiedColnames = NULL, pathToOutput = "", blnkReplicates = FALSE,
  numberOfReplicates)

Arguments

data	data formatted by the use of the mergeDataSet function from LipidQ.
endogene_lipid_db	the endogene lipid database
ISTD_lipid_db	the ISTD lipid database
userSpecifiedColnames	the column names template file containing user specified column names for the input data.
pathToOutput	the directory path to save the plots
blnkReplicates	logical parameter for specifying whether the blank sample contains replicates or not. FALSE: no replicates, TRUE: replicates.
numberOfReplicates	the number of replicates for each sample

Value

barplots of every ISTD which includes all samples as well as one barplot of all ISTD with median sample intensity value

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 is sorted mergedDataSet made by using the mergeDataSets() function
mergedDataSetsIsSorted <- read.table(system.file("extdata/dataTables/checks",
 "mergedDataSets.csv", package = "lipidQ"),
 stringsAsFactors = FALSE, header = TRUE, sep = ",")

# create QC plot of ISTD's
plotQC_ISTD(data = mergedDataSetsIsSorted,
 endogene_lipid_db = endogene_lipid_db, ISTD_lipid_db = ISTD_lipid_db,
 userSpecifiedColnames = userSpecifiedColnames,
 pathToOutput = "",
 blnkReplicates = TRUE, numberOfReplicates = 1)

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