qc_plasmid_histogram: Create a histogram with plasmid log2 CPM values and ascertain...

In gimap: Calculate Genetic Interactions for Paired CRISPR Targets

Create a histogram with plasmid log2 CPM values and ascertain a cutoff for low values

Description

Find the distribution of plasmid (day0 data) pgRNA log2 CPM values, and ascertain a cutoff or filter for low log2 CPM values. Assumes the first column of the dataset is the day0 data; do I need a better method to tell, especially if there are reps?

Usage

qc_plasmid_histogram(
  gimap_dataset,
  cutoff = NULL,
  filter_plasmid_target_col = NULL,
  wide_ar = 0.75
)

Arguments

gimap_dataset	The special gimap_dataset from the 'setup_data' function which contains the 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
wide_ar	aspect ratio, default is 0.75

Value

a ggplot histogram

Examples

## Not run: 

gimap_dataset <- get_example_data("gimap")

qc_plasmid_histogram(gimap_dataset)

# or to specify a "cutoff" value that will be displayed as a dashed vertical line
qc_plasmid_histogram(gimap_dataset, cutoff = 1.75)

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

# or to specify a "cutoff" value that will be displayed as a dashed vertical
# line as well as to specify a different column (or set of columns) to select
qc_plasmid_histogram(gimap_dataset, cutoff = 2, filter_plasmid_target_col = 1:2)

## End(Not run)

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