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 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).

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))
#> $depth
#>                               m              dep
#> 908108_H_diadema_Gatokae     m3 11.8653846153846
#> 908150_H_dinops_Guadalcanal  m3 6.77777777777778
#> 908151_H_diadema_Guadalcanal m3 60.8823529411765
#> 908152_H_diadema_Guadalcanal m3         31.28125
#> 908153a_H_dinops_Guadalcanal m3 138.835616438356
#> 908154_H_dinops_Guadalcanal  m3 11.9322033898305
#> 908155_H_dinops_Guadalcanal  m3 22.4920634920635
#> 908156_H_diadema_Guadalcanal m3 82.5072463768116
#> 908208_H_diadema_Guadalcanal m3 18.5254237288136
#> KVO150_H_diadema_Isabel      m3             4.75
#> KVO168_H_diadema_Isabel      m3 9.92682926829268
#> KVO169_H_diadema_Isabel      m3 14.6734693877551
#> KVO170_H_diadema_Isabel      m3 20.3728813559322
#> KVO171_H_diadema_Isabel      m3 8.63414634146342
#> KVO172_H_diadema_Isabel      m3             6.95
#> KVO242_H_dinops_Isabel       m3 29.0461538461538
#> KVO243_H_dinops_Isabel       m3 37.5507246376812
#> KVO244_H_dinops_Isabel       m3 72.2857142857143
#> KVO245_H_dinops_Isabel       m3 80.5070422535211
#> 
#> $snp
#>    var snps
#> 1   m3   52
#> 2   m3   18
#> 3   m3   68
#> 4   m3   64
#> 5   m3   73
#> 6   m3   59
#> 7   m3   63
#> 8   m3   69
#> 9   m3   59
#> 10  m3    8
#> 11  m3   41
#> 12  m3   49
#> 13  m3   59
#> 14  m3   41
#> 15  m3   20
#> 16  m3   65
#> 17  m3   69
#> 18  m3    7
#> 19  m3   71
#> 
#> $loci
#>    var poly.loci
#> 1   m3        52
#> 2   m3        18
#> 3   m3        68
#> 4   m3        64
#> 5   m3        73
#> 6   m3        59
#> 7   m3        63
#> 8   m3        69
#> 9   m3        59
#> 10  m3         8
#> 11  m3        41
#> 12  m3        49
#> 13  m3        59
#> 14  m3        41
#> 15  m3        20
#> 16  m3        65
#> 17  m3        69
#> 18  m3         7
#> 19  m3        71
#> 
#> $snp.R80
#>   var snps.80
#> 1  m3      28
#> 
#> $loci.R80
#>   var poly.loci.80
#> 1  m3           28
#>