Create a filter for pgRNAs which have a low log2 CPM value for the plasmid/Day 0 sample/time point

Source: R/02-gimap_filter.R

This function flags and reports which and how many pgRNAs have low log2 CPM values for the plasmid/Day 0 sample/time point. If more than one column is specified as the plasmid sample, we pool all the replicate samples to find the lower outlier and flag constructs for which any plasmid replicate has a log2 CPM value below the cutoff

qc_filter_plasmid(
  gimap_dataset,
  cutoff = NULL,
  filter_plasmid_target_col = NULL
)

Arguments

gimap_dataset

The special gimap_dataset from the `setup_data` function which contains the log2 CPM transformed data

cutoff

default is NULL, the cutoff for low log2 CPM values for the plasmid time period; if not specified, The lower outlier (defined by taking the difference of the lower quartile and 1.5 * interquartile range) is used

filter_plasmid_target_col

default is NULL, and if NULL, will select the first column only; this parameter specifically should be used to specify the plasmid column(s) that will be selected

Value

a named list with the filter `filter` specifying which pgRNAs have low plasmid log2 CPM (column of interest is `plasmid_cpm_filter`) and a report df `reportdf` for the number and percent of pgRNA which have a low plasmid log2 CPM

Examples

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

qc_filter_plasmid(gimap_dataset)

# or to specify a cutoff value to be used in the filter rather than the lower outlier default
qc_filter_plasmid(gimap_dataset, cutoff = 2)

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

# or to specify a cutoff value that will be used in the filter rather than
# the lower outlier default as well as to specify a different column (or set of columns) to select
qc_filter_plasmid(gimap_dataset, cutoff = 1.75, filter_plasmid_target_col = 1:2)
}