metRead: metRead

In ethevenot/metabolis: Metabolomics Data Analysis

Description

Reading datasets as subfolders containing the 3 tables 'dataMatrix.tsv', 'sampleMetadata.tsv' and 'variableMetadata.tsv'

Usage

metRead(dirC, filesLs = NULL, subsetVc = NA, info.txtC = NA)

Arguments

dirC	Character: directory containing the 3 .tsv files (single dataset), or containing several subdirectories with 3 .tsv files (multiple datasets)
filesLs	List: if dirC is set to NA, the full names of the individual files can be provided; in case of an ExpressionSet, the names of the list must be 'dataMatrix.tsvC', 'sampleMetadata.tsvC', and 'variableMetadata.tsvC' with the corresponding file full names; in case of a MultiDataSet, the list must consists of one such sublist per dataset
subsetVc	Vector of characters: specifying a subset of the subdirectories to be included in the MultiDataSet (by default, all subdirectories containing the 3 tables will be considered as datasets)
info.txtC	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated

Value

MultiDataSet (multiple dataset) instance

Author(s)

Etienne Thevenot, [e-mail]

Examples

dirC <- system.file("extdata", package="metabolis")
## 1) Single set
sacDirC <- file.path(dirC, "sacurine")
sacSet <- metRead(sacDirC)
# or
sacSet <- metRead(NA,
                  filesLs = list(dataMatrix.tsvC = file.path(sacDirC, "dataMatrix.tsv"),
                                 sampleMetadata.tsvC = file.path(sacDirC, "sampleMetadata.tsv"),
                                 variableMetadata.tsvC = file.path(sacDirC, "variableMetadata.tsv")))
## 2) Multiple sets
prometDirC <- file.path(dirC, "promet")
prometMset <- metRead(prometDirC)
metMset <- metRead(prometDirC, subsetVc = "metabo")
# or
prometMset <- metRead(NA,
                       filesLs = list(metabo = list(dataMatrix.tsvC = file.path(prometDirC, "metabo", "dataMatrix.tsv"),
                                                    sampleMetadata.tsvC = file.path(prometDirC, "metabo", "sampleMetadata.tsv"),
                                                    variableMetadata.tsvC = file.path(prometDirC, "metabo", "variableMetadata.tsv")),
                                      proteo = list(dataMatrix.tsvC = file.path(prometDirC, "proteo", "dataMatrix.tsv"),
                                                    sampleMetadata.tsvC = file.path(prometDirC, "proteo", "sampleMetadata.tsv"),
                                                    variableMetadata.tsvC = file.path(prometDirC, "proteo", "variableMetadata.tsv"))))

ethevenot/metabolis documentation built on June 28, 2019, 1:27 p.m.