R: Calculate inter-distance of genomic regions

rainfallTransform {circlize}

R Documentation

Calculate inter-distance of genomic regions

Description

Calculate inter-distance of genomic regions

Usage

rainfallTransform(region, mode = c("min", "max", "mean", "left", "right"))

Arguments

`region`	Genomic positions. It can be a data frame with two columns which are start positions and end positions on a single chromosome. It can also be a bed-format data frame which contains the chromosome column.
`mode`	How to calculate inter-distance. For a region, there is a distance to the prevous region and also there is a distance to the next region. `mode` controls how to merge these two distances into one value.

Value

If the input is a two-column data frame, the function returnes a data frame with three columns: start position, end position and distance. And if the input is a bed-format data frame, there will be the chromosome column added.

The row order of the returned data frame is as same as the input one.

References

Gu, Z. (2014) circlize implements and enhances circular visualization in R. Bioinformatics.

Examples

bed = generateRandomBed()
bed = subset(bed, chr == "chr1")
head(rainfallTransform(bed))

[Package circlize version 0.4.3 Index]