read_samples

pylluminator.samples.read_samples(datadir: str | PathLike | MultiplexedPath, sample_sheet_df: DataFrame | None = None, sample_sheet_name: str | None = None, annotation: Annotations | None = None, max_samples: int | None = None, min_beads=1, keep_idat=False) → Samples | None

Search for idat files in the datadir through all sublevels.

The idat files are supposed to match the information from the sample sheet and follow this naming convention: *[sentrix ID]*[sentrix position]*[channel].idat where * can be any characters. channel must be spelled Red or Grn.

Parameters:

  • datadir (str | os.PathLike | MultiplexedPath) – directory where sesame files are

  • sample_sheet_df (pandas.DataFrame | None) – samples information. If not given, will be automatically rendered. Default: None

  • sample_sheet_name (str | None) – name of the csv file containing the samples’ information. You cannot provide both a sample sheet dataframe and name. Default: None

  • annotation (Annotations | None) – probes information. Default None.

  • max_samples (int | None) – set it to only load N samples to speed up the process (useful for testing purposes). Default: None

  • min_beads (int) – filter probes that have less than N beads. Default: 1

  • keep_idat – if set to True, keep idat data after merging the annotations. Default: False

Type:

bool

Returns:

Samples object or None if an error was raised

Return type:

Samples | None