snps_pairwaise: Direct SNPs pairwaise.
In irycisBioinfo/PATO: Pangenome Analysis Toolkit

snps_pairwaise

R Documentation

Direct SNPs pairwaise.

Description

This function calculates All-vs-All SNPs number. At different of core_snps_matrix this function calculates the raw number of SNPs among each pair of sequences avoiding the bias of the core genome size and/or reference. However, this function is an O(N²) so can be very slow for large datasets.

Usage

snps_pairwaise(file_list, type, n_cores, norm = T)

Arguments

`file_list`	Data frame with the full path to the nucleotide genome files (gene or genomes) or a gff_list object.
`type`	Just for gff_list objects. You must especified if you want to use whole genome sequences "wgs" or genes "nucl"
`n_cores`	Number of cores to use.
`norm`	The output is normalized by the length of the alignment. If norm is TRUE then the output in "SNPs per Megabase". If norm is FALSE then thr output is the raw number of SNPs.