valOutlier¶

besca.pp.valOutlier(adata, nmads=3, rlib_loc='')[source]¶

Estimates and returns the thresholds to use for gene/cell filtering based on outliers calculated from the deviation to the median QCs. Wrapper function based on ‘isOutlier’ function of the ‘scater’ R package.

Parameters:

adata (AnnData) – Unfiltered AnnData object of RNA counts.
nmads (int) – Number of median absolute deviation to use as threshold for outlier detection. Lenient NMADS (3 to 5) generally yield the best results.
rlib_loc (str) – R library location that will be added to the default .libPaths() to locate the required packages.

Return type:

The estimated parameters to set in the besca workflow considering the QC distribution.

Deprecated since version 2.5: This will be removed in 3.0. This R-based function is marked deprecated and will be removed in future versions of besca!