import_topdom_regions: Import all test-set TopDom regions into a single data.frame

In HenrikBengtsson/TopDomStudy: TopDom Study by Segal et al.

Description

This script will read all available ‘topdomData/*/*.rds’ files, extract the TopDom regions for the test samples (but not the reference) and convert to a data.frame with additional columns on parameter settings and RNG seeds appended. All these data.frames are stacked into one big data.frame which is saved to a ‘overlapScoreData/*,test-topdom.rds’.

Usage

import_topdom_regions(
  pattern = paste(c("human,HAP1,unique", "bin_size=.*", "partition_by=cells_by_half",
    "min_cell_size=2", "window_size=.*", "test=.*", "mainseed=0xBEEF"), collapse = ","),
  path = "topdomData",
  skip = TRUE,
  save_individual = TRUE
)

Arguments

pattern	(character string) A regular expression of the subfolders in folder path to import.
path	(character string) The root folder of the overlap score data.
skip	(logical) If TRUE, already existing results are returned, otherwise not.
save_individual	(logical) If TRUE, also the imported data.frames of the subfolders are saved in individual ‘*,test-topdom.rds’ file in the path folder.

Value

The pathname of the saved ‘*,test-topdom.rds’ file in the path folder.

HenrikBengtsson/TopDomStudy documentation built on May 14, 2021, 1:49 p.m.