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"),
        normalize_to_width = FALSE)

### 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.
`normalize_to_width` | If it is `TRUE`, the value is the relative distance divided by the width of the region.

### 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 0.4.5 Index]