merge_bed: Merge overlapping intervals

In haizi-zh/bioessentials: Home-made essential tools for bioinformatics project

Description

This operation is similar to bedtools merge.

Usage

merge_bed(x, max_dist = 0, operation = NULL)

Arguments

x	A data.table object.
max_dist	Maximum distance between features allowed for features to be merged. Default is 0. That is, overlapping and/or book-ended features are merged.
operation	Specify what operations should be applied to merged intervals. Default is NULL, i.e. do not apply any operation and only return the first three columns (chrom, start, end). Must be a list in the following format: list(col1 = func1, col2 = func2, ...), where col1 and col2 are column names, and func1 and func2 are univariate functions applied on the corresponding columns. For example: list(score = sum) means for all intervals merged into one group, take the sum of the score column. Similar to bedtools merge's -c and -o arguments.

Value

A data.table object containing merged intervals.

See Also

https://bedtools.readthedocs.io/en/latest/content/tools/merge.html

Examples

merge_bed(x, operation = list(score = mean))

haizi-zh/bioessentials documentation built on April 10, 2021, 2:34 p.m.