Validate detected duplicates

This function will validate the detected duplicated-SNPs using a moving window approach (see details)

Usage

dup.validate(d.detect, window.size = 100, scaf.size = 10000)

Arguments

d.detect

a data frame of detected duplicates or deviants from the outputs of dupGet or cnv (output of dupGet)

window.size

numerical. a single value of the desired moving window size (default 100 bp)

scaf.size

numerical. scaffold size to be checked. i.e. the split size of the fragment to be checked with the specified window size. default=10000

Value

A data frame of scaffold names and their average presence in the scaffold.

Details

Chromosome positions correctly ordered according to a reference sequence is necessary for this function to work properly. Therefore, this function is still in development for non-mapped reference sequences.

Author

Piyal Karunarathne