run_activity_tests: Run MPRA activity tests
In andrewGhazi/malacoda: Bayesian Analysis of High-Throughput Genomic Assays

Description Usage Arguments Details Value Note Examples

View source: R/traditional_analysis_functions.R

Given a set of MPRA activity measurements, run significance tests to see if there's a difference in activity tests between alleles

run_activity_tests(
  mpra_activities,
  test_type = "t",
  compute_FDR = TRUE,
  plot_p_hist = TRUE
)

`mpra_activities`	a "tall" data frame of MPRA activities
`test_type`	a string indicating the type of test to use to compare activities, either 't' or 'U'
`compute_FDR`	logical indicating whether or not to add on a column of FDR q-values
`plot_p_hist`	logical indicating whether or not to plot a histogram of p-values

Compute activity tests by MPRA variant, comparing the activity measurements between alleles across all sequencing samples.

a data frame of test statistics

These tests assume that after depth correction, MPRA activities are identically distributed across sequencing samples. Thus activities for the same barcodes across different samples are considered as independent measurements.