compute_activities: Compute MPRA activities

In andrewGhazi/malacoda: Bayesian Analysis of High-Throughput Genomic Assays

Description

This function computes traditional MPRA activities, i.e. the log-ratio of RNA to DNA, for each barcode-RNA sample

Usage

compute_activities(
  mpra_data,
  rep_cutoff = 0.15,
  plot_rep_cutoff = TRUE,
  verbose = TRUE
)

Arguments

mpra_data	a data frame of MPRA data
rep_cutoff	a DNA representation cutoff
plot_rep_cutoff	a logical indicating whether or not to plot the DNA barcode abundance and the applied representation cutoff
verbose	logical indicating whether to print messages

Value

a data frame of activities

Note

the output is returned in a "tall" format, with sample_id's gathered into one column

Examples

compute_activities(umpra_example)

andrewGhazi/malacoda documentation built on Aug. 2, 2020, 12:54 a.m.