genome_complement {tidygenomics}

Calculates the complement to the intervals covered by the intervals in a data frame. It can optionally take a chromosome_size data frame that contains 2 or 3 columns, the first the names of chromosome and in case there are 2 columns the size or first the start index and lastly the end index on the chromosome.

Description

Calculates the complement to the intervals covered by the intervals in a data frame. It can optionally take a chromosome_size data frame that contains 2 or 3 columns, the first the names of chromosome and in case there are 2 columns the size or first the start index and lastly the end index on the chromosome.

Usage

genome_complement(x, chromosome_size = NULL, by = NULL)

Arguments

x

A data frame for which the complement is calculated

chromosome_size

A dataframe with at least 2 columns that contains first the chromosome name and then the size of that chromosome. Can be NULL in which case the largest value per chromosome from x is used.

by

A character vector with 3 entries which are the chromosome, start and end column. For example: by=c("chr", "start", "end")

Examples

library(dplyr)

x1 <- data.frame(id = 1:4, bla=letters[1:4],
                 chromosome = c("chr1", "chr1", "chr2", "chr1"),
                 start = c(100, 200, 300, 400),
                 end = c(150, 250, 350, 450))

genome_complement(x1, by=c("chromosome", "start", "end"))