adjust.coordinates {bedr} | R Documentation |
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)
[Package bedr version 1.1.3 Index]