phantom_purger: A function wraper for running the PhantomPurgeR workflow in a...

In csglab/PhantomPurgeR: PhantomPurgeR

A function wraper for running the PhantomPurgeR workflow in a single step.

Description

A function wraper for running the PhantomPurgeR workflow in a single step.

Usage

phantom_purger(
  samples,
  torc,
  max_r = NULL,
  barcode_length = NULL,
  min_umi_cell = 1,
  return_readcounts = FALSE,
  return_discarded = TRUE
)

Arguments

samples	A named list of filepaths
torc	TOR cutoff
max_r	Maximum PCR duplication level to consider
barcode_length	the length of the cell barcode for v2 data
min_umi_cell	The minimum number of UMIs associated with a cell barcode. Barcodes with fewer UMIs are discarded. Default is 1 (i.e. all cell barcodes are retained). For large datasets with many samples set to a larger value (50-200) to reduce memory requirements.
return_readcounts	If true the joined readcounts is returned
return_discarded	return discarded data

Value

out list pf umi_counts, metadata, and summary statistics

csglab/PhantomPurgeR documentation built on July 27, 2023, 8:05 a.m.