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Construct a multiOmicDataSet object from text files (e.g. TSV, CSV).

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

Wraps MOObject::create_multiOmicDataSet_from_files() to add a "colors" analysis if it is not already present.

Usage

create_multiOmicDataSet_from_files(
  sample_meta_filepath,
  feature_counts_filepath,
  count_type = "raw",
  sample_id_colname = NULL,
  feature_id_colname = NULL,
  delim = NULL,
  ...
)

Arguments

sample_meta_filepath

path to text file with sample IDs and metadata for differential analysis.

feature_counts_filepath

path to text file of expected feature counts (e.g. gene counts from RSEM).

count_type

type to assign the values of counts_dat to in the counts slot

sample_id_colname

name of the column in sample_metadata that contains the sample IDs. (Default: NULL - first column in the sample metadata will be used.)

feature_id_colname

name of the column in counts_dat that contains feature/gene IDs. (Default: NULL - first column in the count data will be used.)

delim

Delimiter used in the input files. Any delimiter accepted by readr::read_delim() can be used. If the files are in CSV format, set delim = ','; for TSV format, set delim = '\t'.

...

additional arguments forwarded to readr::read_delim().

Value

A MOObject::multiOmicDataSet object.

See also

MOObject::create_multiOmicDataSet_from_files()

Other moo IO: create_multiOmicDataSet_from_dataframes(), multiOmicDataSet(), read_multiOmicDataSet(), read_multiOmicDataSet_properties(), write_multiOmicDataSet(), write_multiOmicDataSet_properties()