Calculate motifbreakR p-values — MOTIFBREAKR_calc

Calculate p-values for each motifbreakR motif disruption result.

MOTIFBREAKR_calc_pvals(
  mb_res,
  background = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
  granularity = NULL,
  nThread = 1,
  results_dir = file.path(tempdir(), "results"),
  verbose = TRUE
)

Arguments

mb_res: Results generated by MOTIFBREAKR, in GRanges format.
background: Numeric Vector; the background probabilities of the nucleotides
granularity: Numeric Vector; the granularity to which to round the PWM, larger values compromise full accuracy for speed of calculation. A value of NULL does no rounding.
nThread: Number of threads to parallelize analyses across.
results_dir: Directory where results should be saved as a file named: <results_dir>/_genome_wide/motifbreakR/motifbreakR_results.rds. If NULL, results will not be saved to disk.
verbose: Print messages.

Value

Motif disruption predictions in

GRanges format, with the p-value columns filled out.

Examples

 
mb_res <- MOTIFBREAKR(rsid_list = c("rs11175620"),
                      # limit the number of datasets tests 
                      # for demonstration purposes only
                      pwmList_max = 5)
#> genome_build set to hg19 by default.
#> Using genome_build hg19
#> + MOTIFBREAKR:: Using pre-existing tmp file.
mb_res_p <- MOTIFBREAKR_calc_pvals(mb_res = mb_res)                       
#> + MOTIFBREAKR:: Calculating p-values for 1 RSID(s)...
#> + MOTIFBREAKR:: Saving updated results ==> /tmp/Rtmp3k34Cf/results/_genome_wide/motifbreakR/motifbreakR_results.rds