RowWiseSplit: RowWiseSplit

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

RowWiseSplit

Description

Performing the correlation or Fisher test association for a SummarizedExperiment object requires extreme amounts of memory. To reduce the amount of memory necessary, we instead get the individual rows from the consensus assay. We can then remove the NoCalls (no reads) from the individual vectors, further reducing the amount of memory needed.

When the NoCalls are removed, the repective cells are also removed if a different assay is selected.

Usage

RowWiseSplit(
  se,
  n_cores = 1,
  assay_to_split = "consensus",
  remove_nocalls = TRUE
)

Arguments

se	SummarizedExperiment object.
n_cores	Number of cores to use.
assay_to_split	Which assay to you want to split?
remove_nocalls	Do you want to remove NoCall cells?

CostaLab/sigurd documentation built on Feb. 10, 2025, 11:08 p.m.