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Create a Biobase set object to store omics data

Source: R/create_omics_sets.R
create_omics_set.Rd

Creates a Biobase object to store an omics dataset and associated samples and features metadata.

Usage

create_omics_set(
  dataset,
  omics_type = c("phenomics", "genomics", "transcriptomics", "metabolomics"),
  features_metadata = NULL,
  samples_metadata = NULL
)

Arguments

dataset

Matrix, the omics dataset in matrix form with features as rows and samples as columns.

omics_type

Character, which type of omics data is being stored? Possible values are 'genomics', 'transcriptomics', 'metabolomics' and 'phenomics'. Use 'phenomics' for any other omics.

features_metadata

Data.frame, a feature annotation data-frame with features as rows and information about the features as columns. The number of rows and row names must match those of the dataset matrix.

samples_metadata

Data.frame, a samples information data-frame with samples as rows and information about the samples as columns. The number of rows and row names must match the number of columns and column names of the dataset matrix.

Value

An object derived from Biobase::eSet:

  • if omics_type = 'genomics': a Biobase::SnpSet object;

  • if omics_type = 'transcriptomics': a Biobase::ExpressionSet object.

  • if omics_type = 'metabolomics': a MetabolomeSet object.

  • if omics_type = 'phenomics' a PhenotypeSet object.

Examples

if (FALSE) { # \dontrun{
data_geno <- import_dataset_csv(
"genotype_dataset.csv",
  col_id = "Marker",
  features_as_rows = TRUE
)
geno_info_features <- import_fmetadata_csv(
"genotype_features_info.csv",
  col_id = "Marker"
)
samples_information <- import_smetadata_csv(
"samples_information.csv",
  col_id = "Sample"
)
create_omics_set(
  dataset = data_geno,
  omics_type = "genomics",
  features_metadata = geno_info_features,
  samples_metadata = samples_information
)
} # }