Import a dataset from a csv file — import_dataset

Reads a csv file and returns a matrix in which the rows corresponds to features (e.g. markers, genes, phenotypes...) and the columns correspond to samples/observations.

Usage

import_dataset_csv(file, col_id, features_as_rows = TRUE, ...)

Arguments

file: Character, path to the dataset csv file.
col_id: Character, the name of the column in the file that contains the ID of the rows (i.e. feature IDs if features_as_rows is TRUE, or sample IDs if features_as_rows is FALSE).
features_as_rows: Logical, do the rows in the file correspond to features? Default value is TRUE, i.e. the file contains features as rows and samples as columns.
...: Further arguments passed to readr::read_csv().

Value

A matrix with the samples as columns and the features as rows. Feature IDs are used as row names and sample IDs as column names.

Examples

if (FALSE) { # \dontrun{
data_geno <- import_dataset_csv(
  "genotype_dataset.csv",
  col_id = "Marker",
  features_as_rows = TRUE
)
data_pheno <- import_dataset_csv(
  "phenotype_dataset.csv",
  col_id = "Sample",
  features_as_rows = FALSE
)
} # }