Optimize the n parameter during denovo stacks assembly

This function requires the path to stacks vcf file(s) as input. There are slots for varying the n parameter across M-1, M, and M-1 (as recommended by Paris et al. 2017). After running stacks with each of the n options, plug the output vcf files into this function to visualize the effect of varying m on number of SNPs and loci built to recognize which value optimizes the n parameter for your dataset at the 'R80' cutoff (Paris et al. 2017).

optimize_n(nequalsMminus1 = NULL, nequalsM = NULL, nequalsMplus1 = NULL)

Arguments

nequalsMminus1	Path to the input vcf file for a run when n=M-1
nequalsM	Path to the input vcf file for a run when n=M
nequalsMplus1	Path to the input vcf file for a run when n=M+1

Value

A dataframe showing the number of SNPs and loci retained across filtering levels for each n value

Examples

optimize_n(nequalsM =
system.file("extdata","nequalsm.vcf.gz",package="RADstackshelpR",mustWork=TRUE))
#> $snp
#>    var snps
#> 1  n=M   32
#> 2  n=M    8
#> 3  n=M   40
#> 4  n=M   40
#> 5  n=M   39
#> 6  n=M   29
#> 7  n=M   32
#> 8  n=M   39
#> 9  n=M   31
#> 10 n=M    4
#> 11 n=M   18
#> 12 n=M   33
#> 13 n=M   38
#> 14 n=M   22
#> 15 n=M    9
#> 16 n=M   34
#> 17 n=M   38
#> 18 n=M    1
#> 19 n=M   41
#> 
#> $loci
#>    var poly.loci
#> 1  n=M        32
#> 2  n=M         8
#> 3  n=M        40
#> 4  n=M        40
#> 5  n=M        39
#> 6  n=M        29
#> 7  n=M        32
#> 8  n=M        39
#> 9  n=M        31
#> 10 n=M         4
#> 11 n=M        18
#> 12 n=M        33
#> 13 n=M        38
#> 14 n=M        22
#> 15 n=M         9
#> 16 n=M        34
#> 17 n=M        38
#> 18 n=M         1
#> 19 n=M        41
#> 
#> $snp.R80
#>   var snps.80
#> 1 n=M      17
#> 
#> $loci.R80
#>   var poly.loci.80
#> 1 n=M           17
#>