Create a filter for pgRNAs which have a raw count of 0 for any sample/time point

Source: R/02-gimap_filter.R

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

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

if (FALSE) {
gimap_dataset <- get_example_data("gimap")
qc_filter_zerocounts(gimap_dataset)

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