R/jaccard.R

# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
# (either version 1, or at your option, any later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text.
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jaccard <- function(x, y, proportion.overlap  = 1e-9, reciprocal.overlap = FALSE, check.zero.based = TRUE, check.chr = TRUE, check.valid = TRUE, check.sort = TRUE, check.merge = TRUE, verbose = TRUE){

	catv("JACCARD METRIC\n");

	params <- paste0("-f ", proportion.overlap);

	if (reciprocal.overlap) {
		params <- paste0(params, " -r");
		}

	x <- bedr(engine = "bedtools", input = list(a = x, b=y), method = "jaccard", params = params, check.zero.based = check.zero.based, check.chr = check.chr, check.valid = check.valid, check.sort = check.sort, check.merge = check.merge, verbose = verbose);

#	colnames(x) <- c("intersection", "union", "jaccard", "n.intersections");;

	return(x);
	}

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bedr documentation built on May 2, 2019, 11:36 a.m.