optimize_m: Optimize the m parameter during denovo stacks assembly

In RADstackshelpR: Optimize the De Novo Stacks Pipeline via R

Description

This function requires the path to stacks vcf file(s) as input. There are slots for varying the m parameter from 3-7 (as recommended by Paris et al. 2017). After running stacks with each of the m options, plug the output vcf files into this function to calculate the effect of varying m on depth and number of SNPs/loci built. Plug the output of this function into vis_loci() to visualize the optimal the m parameter for your dataset at the 'R80' cutoff (Paris et al. 2017).

Usage

optimize_m(m3 = NULL, m4 = NULL, m5 = NULL, m6 = NULL, m7 = NULL)

Arguments

m3	Path to the input vcf file for a run when m=3
m4	Path to the input vcf file for a run when m=4
m5	Path to the input vcf file for a run when m=5
m6	Path to the input vcf file for a run when m=6
m7	Path to the input vcf file for a run when m=7

Value

A list containing five summary dataframes, 'depth' showing depth per sample for each m value, 'snp' showing the number of non-missing SNPs retained in each sample at each m value, 'loci' showing the number of non-missing loci retained in each sample at each m value, 'snp.R80' showing the total number of SNPs retained at an 80% completeness cutoff, and 'loci.R80' showing the total number of polymorphic loci retained at an 80% completeness cutoff.

Examples

optimize_m(m3=system.file("extdata","m3.vcf.gz",package="RADstackshelpR",mustWork=TRUE))

RADstackshelpR documentation built on Aug. 19, 2021, 5:06 p.m.