rankSimilarity: Ranks the similarities between a given query bed file with...

Description Usage Arguments Value

View source: R/rankSimilarity.R

Description

The function compares a given query bed file with multiple bed files (database files), and ranks the relative similarity between each file pairing, computed using jaccard indexes, where 0 has no similarities and 1 has an identical file. The function can also provide a significance value (p-value) of the similarity index based on user selection.

Usage

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rankSimilarity(
  queryBed = queryBed,
  database_dir = database_dir,
  output_path = output_path,
  output_frm_DatabaseFileSize = output_frm_DatabaseFileSize
)

Arguments

queryBed

The file path of a query bed file to be compared to the database files.

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.

output_frm_DatabaseFileSize

The file was generated from "DatabaseFileSize" function. Please also include the directory path of this file. The file contains the two columns: 1) BED file names in the database, and 2) pre-calculated length of binding sizes for each BED file

Value

A dataframe that shows the similarities of the query file to the database files ranked from greatest to least.


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