bedr (version 1.1.3)

adjust.coordinates: 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)

Value

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

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

Author

Helena Winata

Examples

if (FALSE) {
  coordsA <- adjust.coordinates(x, 'CIPOS', x$POS, x$POS);
  coordsB <- adjust.coordinates(x, 'CIEND', x$END, x$END)
  }