adjust.coordinates: adjust coordinates for a BEDPE file

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

adjust coordinates for a BEDPE file

Description

Adjust coordinates for a breakpoint in dataframe using confidence intervals specified an INFO field in the VCF file, if it exists. Used in the 'vcf2bedpe' function.

Usage

adjust.coordinates(df, info_tag, start, end)

Arguments

df	a dataframe object obtained from a VCF file
info_tag	an info tag from the dataframe/VCF file, e.g. 'CIPOS' or 'CIEND'
start	VCF column containing the start coordinate
end	VCF column containing the end coordinate

Value

a named list of the adjusted start and end coordinates of a breakpoint.

Author(s)

Helena Winata

Examples

## Not run: 
  coordsA <- adjust.coordinates(x, 'CIPOS', x$POS, x$POS);
  coordsB <- adjust.coordinates(x, 'CIEND', x$END, x$END)
  
## End(Not run)

bedr documentation built on April 11, 2025, 5:52 p.m.