mergeDataSets: Merge Data Sets

In ELELAB/lipidQ: Lipidomics Analysis Tool

Description

This function merges multiple data sets together. The data sets are listed in the dataList parameter.

Usage

mergeDataSets(dataList, endogene_lipid_db, ISTD_lipid_db,
  userSpecifiedColnames = NULL, correctionList = NULL, multiply = NULL)

Arguments

dataList	a list of paths referring to input data
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. is used to translate the user specified column names to the program, so that it uses the correct columns for the different analysis procedures.
correctionList	a file containing a list of sum compositions to be multiplied for in the MS1 column values (intensity values)
multiply	a parameter used to multiply intensity values in the MS1 column on selected sum compositions. The parameter is useful if lipidX is used to obtain the intensity data derived from overlapping MS scan ranges. The sum composition are selected by the user and should appear in a correction list file that is used as argument for the correctionList parameter.

Value

a data set consisting of merged input data

Author(s)

André Vidas Olsen

Examples

# make input data path list
dataPathList <- c(system.file("extdata/mE504_Data",
                  "mE504_NEG_High-out.csv", package = "lipidQ"),
                 system.file("extdata/mE504_Data",
                  "mE504_NEG_Low-out.csv", package = "lipidQ"),
                 system.file("extdata/mE504_Data",
                  "mE504_POS_High-out.csv", package = "lipidQ"),
                 system.file("extdata/mE504_Data",
                  "mE504_NEG_Low-out.csv", package = "lipidQ"))

# load endo & ISTD databases as well as user specified column names file.
endogene_lipid_db <- read.table(system.file("extdata/LipidQ_DataBase",
 "LP_DB_MS1_v1.csv", package = "lipidQ"), stringsAsFactors = FALSE,
 header = TRUE, sep = ",")

ISTD_lipid_db <- read.table(system.file("extdata/LipidQ_DataBase",
 "ISTD_LP_DB_MS1_v1.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 = ",")

# merge input data sets into one file
mergeDataSets(dataList = dataPathList, endogene_lipid_db = endogene_lipid_db,
 ISTD_lipid_db = ISTD_lipid_db, userSpecifiedColnames =
 userSpecifiedColnames)

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