count_matrix_stats: Build count matrix statistics

In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses

Build count matrix statistics

Description

Calculate common CRISPR statistics from a count matrix

Usage

count_matrix_stats(
  count_matrix = NULL,
  id_column = 1,
  gene_column = 2,
  count_column = 3,
  low_counts = 30,
  total_reads = NULL
)

Arguments

count_matrix	a count matrix data frame.
id_column	the index of column containing unique sgRNA identifiers.
gene_column	the index of column containing gene symbols.
count_column	the index of column containing counts.
low_counts	a threshold below which counts are considered low (default: 30).
total_reads	a vector of read totals with samples as names.

Details

Optionally, total read counts can be given as a vector to total_reads with sample names as names for adding total reads (total_reads), proportion of mapped reads (prop_mapped_reads) and percentage of mapped reads (pct_mapped_reads).

cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.