indivPVal: Calculate significance of bed file similarity

In Bao-Lab/GPSmatch: Compares and Ranks the Similarities of Bed Files

Description

The function compare two bed files (query and hit) to check if the observed degree of similarity between the query and the hit files may occur purely by chance.

Usage

indivPVal(
  n = 2000,
  bed1 = bed1,
  genome = genome,
  bed2 = bed2,
  output_path = output_path
)

Arguments

n	The number of background files generated in order to compute the p-value. As the n increases, the p-value will become more reliable, but the user should be aware that this will significantly increase the computing time. We have set a default n of 2000.
bed1	The file path of a query bed file to be compared to the database files.
genome	The file path of a genome file, which should be tab delimited and structured as follows: <chromName><TAB><chromSize>. A pre-formatted hg19 genome file can be found on the Github.
bed2	The file path of a bedfile in the database, or any bed file.
output_path	The file path where the output .csv file will be generated

Value

A .csv file showing the p-value, pi-score, and a five number summary of the background file distribution compared to the original jaccard index.

Examples

indivPVal(n=n,bed1="/dir/bed1.txt",genome ="/dir/genome.txt",bed2 ="/dir/bed2.txt", output_path = "/dir/output_folder")

Bao-Lab/GPSmatch documentation built on Dec. 17, 2021, 10:45 a.m.