reading: reading

In SciDoPhenIA/phenomis: Analysis of single and multiple phenomic data sets

reading

Description

Reading dataset(s) in the 3 tables 'dataMatrix' (or 'DM'), sampleMetadata' (or 'SM') and variableMetadata' (or 'VM') tabular format. In case of a single dataset (3 tables in the specified directory), a SummarizedExperiment instance is returned. In case of a multiple dataset (several subfolders containing 3 tables), a MultiAssayExperiment instance is created.

Usage

reading(
  dir.c,
  files.ls = NULL,
  subsets.vc = NA,
  output.c = c("exp", "set")[1],
  report.c = c("none", "interactive", "myfile.txt")[2]
)

Arguments

dir.c	character(1): directory containing the 3 tabular files (single dataset), or containing several subdirectories with 3 tabular files (multiple datasets)
files.ls	list: if dir.c is set to NA, the full names of the individual files can be provided; in case of a SummarizedExperiment, the names of the list must be 'dataMatrix', 'sampleMetadata', and 'variableMetadata' with the corresponding file full names; in case of a MultiAssayExperiment, the list must consists of one such sublist per dataset
subsets.vc	character(): specifying a subset of the subdirectories to be included in the MultiAssayExperiment (by default, all subdirectories containing the 3 tables will be considered as datasets)
output.c	character(1): Either 'exp' for SummarizedExperiment (or MultiAssayExperiment), or 'set' for ExpressionSet (or MultiDataSet) output formats (the latter are deprecated)
report.c	character(1): 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

SummarizedExperiment (one dataset) or MultiAssayExperiment (multiple datasets) instance containing the dataset(s)

Examples

data_dir.c <- system.file("extdata", package = "phenomis")
## 1) Single set
sacurine_dir.c <- file.path(data_dir.c, "W4M00001_Sacurine-statistics")
sacurine.se <- reading(sacurine_dir.c)
# or
sacurine.se <- reading(NA,
                  files.ls = list(dataMatrix = file.path(sacurine_dir.c, "Galaxy1_dataMatrix.tabular"),
                                  sampleMetadata = file.path(sacurine_dir.c, "Galaxy2_sampleMetadata.tabular"),
                                  variableMetadata = file.path(sacurine_dir.c, "Galaxy3_variableMetadata.tabular")))
## 2) Multiple sets
prometis_dir.c <- file.path(data_dir.c, "prometis")
prometis.mae <- reading(prometis_dir.c)
metabo.mae <- reading(prometis_dir.c, subsets.vc = "metabolomics")
# or
prometis.mae <- reading(NA,
                       files.ls = list(metabolomics = list(dataMatrix = file.path(prometis_dir.c, "metabolomics", "dataMatrix.tsv"),
                                                           sampleMetadata = file.path(prometis_dir.c, "metabolomics", "sampleMetadata.tsv"),
                                                           variableMetadata = file.path(prometis_dir.c, "metabolomics", "variableMetadata.tsv")),
                                      proteomics = list(dataMatrix = file.path(prometis_dir.c, "proteomics", "dataMatrix.tsv"),
                                                        sampleMetadata = file.path(prometis_dir.c, "proteomics", "sampleMetadata.tsv"),
                                                        variableMetadata = file.path(prometis_dir.c, "proteomics", "variableMetadata.tsv"))))

SciDoPhenIA/phenomis documentation built on June 9, 2022, 11:54 p.m.