Optimize the M parameter during denovo stacks assembly

This function requires the path to stacks vcf file(s) as input. There are slots for varying the M parameter from 1-8 (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 the 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).

optimize_bigM(
  M1 = NULL,
  M2 = NULL,
  M3 = NULL,
  M4 = NULL,
  M5 = NULL,
  M6 = NULL,
  M7 = NULL,
  M8 = NULL
)

Arguments

M1

Path to the input vcf file for a run when M=1
M2

Path to the input vcf file for a run when M=2
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
M8

Path to the input vcf file for a run when M=8

Value

A list containing four summary dataframes, '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_bigM(M1=system.file("extdata","bigM1.vcf.gz",package="RADstackshelpR",mustWork=TRUE))

#> $snp
#>    var snps
#> 1   M1   55
#> 2   M1   19
#> 3   M1   76
#> 4   M1   68
#> 5   M1   82
#> 6   M1   54
#> 7   M1   62
#> 8   M1   78
#> 9   M1   58
#> 10  M1    6
#> 11  M1   36
#> 12  M1   55
#> 13  M1   60
#> 14  M1   43
#> 15  M1   24
#> 16  M1   66
#> 17  M1   71
#> 18  M1    4
#> 19  M1   83
#> 
#> $loci
#>    var poly.loci
#> 1   M1        55
#> 2   M1        19
#> 3   M1        76
#> 4   M1        68
#> 5   M1        82
#> 6   M1        54
#> 7   M1        62
#> 8   M1        78
#> 9   M1        58
#> 10  M1         6
#> 11  M1        36
#> 12  M1        55
#> 13  M1        60
#> 14  M1        43
#> 15  M1        24
#> 16  M1        66
#> 17  M1        71
#> 18  M1         4
#> 19  M1        83
#> 
#> $snp.R80
#>   var snps.80
#> 1  M1      28
#> 
#> $loci.R80
#>   var poly.loci.80
#> 1  M1           28
#>