get_well_represented: Get well represented barcodes
In andrewGhazi/malacoda: Bayesian Analysis of High-Throughput Genomic Assays

Description Usage Arguments Details Note Examples

Identify barcodes well-represented in DNA samples from input MPRA data.

get_well_represented(
  mpra_data,
  sample_depths,
  rep_cutoff,
  plot_rep_cutoff = FALSE,
  verbose = TRUE
)

`mpra_data`	a data frame of MPRA data
`sample_depths`	a data frame of sample depths
`rep_cutoff`	a representation cutoff
`plot_rep_cutoff`	logical indicating whether to plot the DNA representation distribution with the input rep_cutoff indicated
`verbose`	logical indicating to print messages about DNA removal statistics

Use this function to tune the representation cutoff shown on the resulting histogram in order to discard failed and poorly-represented barcodes. These will sometimes be visible as a noticeable bump on the left side of the plot, though carefully prepared oligo libraries my not exhibit this.

After turning, plot_rep_cutoff may be set to FALSE to suppress the plotting.

properly formatted sample_depths can be obtained from get_sample_depths()

example_depths = get_sample_depths(umpra_example)
get_well_represented(umpra_example,
    sample_depths = example_depths,
    rep_cutoff = .15,
    plot_rep_cutoff = TRUE,
    verbose = TRUE)
# The final depth adjusted cutoff value will be lower for non-subsampled
# datasets that have higher total sequencing depth.