pmolCalc: picomol Calculation

In ELELAB/lipidQ: Lipidomics Analysis Tool

Description

This function calculates pico mol (pmol) of species based on intensity from measurements (target specie + internal standard) and known quantity of internal standard

Usage

pmolCalc(data, endogene_lipid_db, ISTD_lipid_db, userSpecifiedColnames = NULL,
  spikeISTD, zeroThresh, LOQ = FALSE, fixedDeviation = 0,
  numberOfReplicates = 1, blnkReplicates = FALSE,
  numberOfInstancesThreshold, thresholdValue)

Arguments

data	input data to be used quantified
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.
spikeISTD	internal standard spike amount in uL
zeroThresh	an optional threshold that determines if a given small value in mol pct. specie composition columns should be rounded down to zero.
LOQ	logical parameter to indicate whether or not limit of quantification (LOQ) threshold is activated.
fixedDeviation	the amount in percentages (-100 - 100) that values has to be above the LOQ threshold
numberOfReplicates	the number of replicates for each sample
blnkReplicates	logical parameter for specifying whether the blank sample contains replicates or not. FALSE: no replicates, TRUE: replicates.
numberOfInstancesThreshold	the number of replicates for a given sample that has to have values above the specified threshold value (thesholdValue)
thresholdValue	user specified threshold value based on technical noise and/or other variation sources. This paramter will determine the threshold in which a replicate will be considered as having an observed value or not.

Value

a data set containing pmol and pmol related columns

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 a filtered data set made by using the filterDataSet() function
filteredDataSet <- read.table(system.file("extdata/dataTables/checks",
 "filteredDataSet.csv", package = "lipidQ"), stringsAsFactors = FALSE,
 header = TRUE, sep = ",")

# calculate pmol for data
pmolCalculatedDataSet <- pmolCalc(data = filteredDataSet,
 endogene_lipid_db = endogene_lipid_db, ISTD_lipid_db = ISTD_lipid_db,
 userSpecifiedColnames = userSpecifiedColnames, spikeISTD = 2,
 zeroThresh = 0.25)

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