Vizualise missing data per SNP, remove SNPs above a missing data cutoff

This function can be run in two ways: 1) Without 'cutoff' specified. This will vizualise the amount of missing data in each sample across a variety of potential missing data cutoffs. Additionally, it will show you dotplots visualizing the number of total SNPs retained across a variety of filtering cutoffs, and the total proportion of missing data. Based on these visualizations, you can make an informed decision on what you think might be an optimal cutoff to minimize the overall missingness of your dataset while still retaining an appropriate amount of SNPs for the downstream inferences you hope to make 2) with 'cutoff' specified. This option will show you the dotplots with the cutoff you set, and then remove SNPs above the missing data cutoff.

missing_by_snp(vcfR, cutoff = NULL)

Arguments

vcfR: a vcfR object
cutoff: a numeric value between 0-1 specifying the maximum proportion of missing data allowed in a SNP to be retained for downstream analyses

Value

if 'cutoff' is not specified, will return a dataframe containing the proportion missing data and the total SNPs retained across each filtering level. If 'cutoff' is specified, SNPs falling above the missing data cutoff will be removed, and the filtered vcfR object will be returned.

Examples

missing_by_snp(vcfR = SNPfiltR::vcfR.example)
#> cutoff is not specified, exploratory visualizations will be generated
#> Picking joint bandwidth of 0.0903


#>    filt missingness snps.retained
#> 1  0.30  0.28741007           417
#> 2  0.50  0.21399417           343
#> 3  0.60  0.17118644           295
#> 4  0.65  0.14907063           269
#> 5  0.70  0.12938776           245
#> 6  0.75  0.11585903           227
#> 7  0.80  0.09698492           199
#> 8  0.85  0.08011696           171
#> 9  0.90  0.06082090           134
#> 10 0.95  0.04414894            94
#> 11 1.00  0.00000000            11
missing_by_snp(vcfR = SNPfiltR::vcfR.example, cutoff = .6)
#> cutoff is specified, filtered vcfR object will be returned
#> 41% of SNPs fell below a completeness cutoff of 0.6 and were removed from the VCF

#> ***** Object of Class vcfR *****
#> 20 samples
#> 1 CHROMs
#> 295 variants
#> Object size: 0.5 Mb
#> 17.12 percent missing data
#> *****        *****         *****