sigEvl: Computes the p-value and pi-scores for top hits from...

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

Description

The function evaluates the significance of the jaccard index scores by calculating p-values and pi-scores.

Usage

sigEvl(
  n = n,
  tophit = tophit,
  genome = genome,
  queryBed = queryBed,
  queryBed_jaccard_output = queryBed_jaccard_output,
  database_dir = database_dir,
  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.
tophit	The number of top hits that the user are interested to compute p-value and pi-scores. Those top hits were generated and ordered by function rankSimilarity() at step 2 and were written to file queryBed_jaccard_output.
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.
queryBed	The file path of a query bed file to be compared to the database files.
queryBed_jaccard_output	The file path of the output file generated from the rankSimilarity() function
database_dir	The directory of a folder containing database files to be used for comparison with the query file.
output_path	The file path where the output .csv file will be generated.

Value

A dataframe that shows the similarities of the query file to the database files ranked from greatest to least, tailored to user method specification.

Examples

sigEvl(n=2000, tophit=5,genome="/dir/genome-file.txt", queryBed="/dir/bed1.txt",queryBed_jaccard_output="/dir/bed1_jaccard_output.txt",database_dir="/dir/database_dir",output_path="/dir/output_path")

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