qc_filter_zerocounts: Filter out samples of zero counts Create a filter for pgRNAs...

In gimap: Calculate Genetic Interactions for Paired CRISPR Targets

Filter out samples of zero counts Create a filter for pgRNAs which have a raw count of 0 for any sample/time # point

Description

This function flags and reports which and how many pgRNAs have a raw count of 0 for any sample/time point

Usage

qc_filter_zerocounts(gimap_dataset, filter_zerocount_target_col = NULL)

Arguments

gimap_dataset	The special gimap_dataset from the 'setup_data' function which contains the raw count data
filter_zerocount_target_col	default is NULL; Which sample column(s) should be used to check for counts of 0? If NULL and not specified, downstream analysis will select all sample columns

Value

a named list with the filter 'filter' specifying which pgRNA have a count zero for at least one sample/time point and a report df 'reportdf' for the number and percent of pgRNA which have a count zero for at least one sample/time point

Examples

gimap_dataset <- get_example_data("gimap", data_dir = tempdir())
qc_filter_zerocounts(gimap_dataset)

# or to specify a different column (or set of columns to select)
qc_filter_zerocounts(gimap_dataset, filter_zerocount_target_col = 1:2)

gimap documentation built on June 8, 2025, 10:13 a.m.