Description Usage Arguments Details Note Examples
View source: R/prior_fitting.R
Identify barcodes well-represented in DNA samples from input MPRA data.
1 2 3 4 5 6 7 | 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()
1 2 3 4 5 6 7 8 | 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.
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.