filter_scd: Perform a series of filters on a single-cell dataset.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Perform a series of filters on a single-cell dataset.

Description

This function should perform a series of relatively consistent filters on a single-cell dataset, with options to play with the various filters and their parameters.

Usage

filter_scd(
  scd,
  min_num_rna = 200,
  max_num_rna = NULL,
  min_pct_ribo = 5,
  max_pct_ribo = NULL,
  remerge = NULL,
  max_pct_mito = 15,
  min_pct_mito = NULL,
  mito_pattern = "^mt-",
  ribo_pattern = "^Rp[sl]",
  min_gene_counts = 3,
  verbose = FALSE
)

Arguments

scd	Single Cell Dataset to filter.
min_num_rna	Drop cells with fewer than this number of observed RNA species.
max_num_rna	An unlikely filter for maximum number of RNAs.
min_pct_ribo	Drop cells with less than this percentage of ribosomal protein RNAs observed.
max_pct_ribo	Drop cells with more than this percentage of ribosomal protein RNAs observed.
remerge	Merge the data back if there are multiple assays.
max_pct_mito	Drop cells with more than this percentage of mitochondrial RNA observed.
min_pct_mito	Drop cells with less than this percentage of mitochondrial RNA observed.
mito_pattern	Regex pattern to search RNA symbols for mitochondrial species.
ribo_pattern	Regex pattern to search RNA symbols for ribosomal protein species.
min_gene_counts	Drop genes across cells which are observed less than this number of times, I don't expect many of these.
verbose	Be chatty about what you are doing?

Value

Filtered scd

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.