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multiOmicDataSet class

Source: R/0_mo-class.R
multiOmicDataSet.Rd

multiOmicDataSet class

Usage

multiOmicDataSet(sample_metadata, anno_dat, counts_lst, analyses_lst = list())

Arguments

sample_metadata

sample metadata as a data frame or tibble. The first column is assumed to contain the sample IDs which must correspond to column names in the raw counts.

anno_dat

data frame of feature annotations, such as gene symbols or any other information about the features in counts_lst.

counts_lst

named list of data frames containing counts, e.g. expected feature counts from RSEM. Each data frame is expected to contain a feature_id column as the first column, and all remaining columns are sample IDs in the sample_meta.

analyses_lst

named list of analysis results, e.g. DESeq results object

Value

A multiOmicDataSet S7 object.

See also

Other moo constructors: create_multiOmicDataSet_from_dataframes(), create_multiOmicDataSet_from_files()

Additional properties

@sample_meta

sample metadata as a data frame or tibble. The first column is assumed to contain the sample IDs which must correspond to column names in the raw counts.

@annotation

data frame of feature annotations, such as gene symbols or any other information about the features in the counts list.

@counts

named list of counts data frames (e.g. raw, clean, cpm, filt, norm, batch). Each data frame is expected to contain a feature ID column as the first column, and all remaining columns are sample IDs.

@analyses

named list of analysis results (e.g. DESeq2 results, colors).