Return QC information to assess loci (MAF, missingness and HWE test).
Usage
qc_report_loci(.x, ...)
# S3 method for class 'tbl_df'
qc_report_loci(.x, ...)
# S3 method for class 'grouped_df'
qc_report_loci(.x, ...)Arguments
- .x
a
gen_tibbleobject.- ...
currently unused the HWE test.
Examples
# Create a gen_tibble of lobster genotypes
bed_file <-
system.file("extdata", "lobster", "lobster.bed", package = "tidypopgen")
example_gt <- gen_tibble(bed_file,
backingfile = tempfile("lobsters"),
quiet = TRUE
)
# Get a QC report for the loci
example_gt %>% qc_report_loci()
#> This gen_tibble is not grouped. For Hardy-Weinberg equilibrium, `qc_report_loci()` will assume individuals are part of the same population and HWE test p-values will be calculated across all individuals. If you wish to calculate HWE p-values within populations or groups, please use`group_by()` before calling `qc_report_loci()`.
#> # A tibble: 79 × 4
#> snp_id maf missingness hwe_p
#> <chr> <dbl> <dbl> <dbl>
#> 1 rs3441 0.328 0.0227 0.440
#> 2 rs4173 0.424 0.0341 0.584
#> 3 rs6157 0.278 0.0284 0.00293
#> 4 rs7502 0.423 0.0455 0.479
#> 5 rs7892 0.101 0.0170 0.305
#> 6 rs9441 0.307 0.0739 0.784
#> 7 rs11071 0.123 0.0284 0.00299
#> 8 rs11183 0.458 0.0568 0.102
#> 9 rs11291 0.244 0.0455 0.000000944
#> 10 rs12971 0.312 0.0625 0.0242
#> # ℹ 69 more rows
# Group by population to calculate HWE within populations
example_gt <- example_gt %>% group_by(population)
example_gt %>% qc_report_loci()
#> # A tibble: 79 × 4
#> snp_id maf missingness hwe_p
#> <chr> <dbl> <dbl> <dbl>
#> 1 rs3441 0.328 0.0227 0.850
#> 2 rs4173 0.424 0.0341 0.546
#> 3 rs6157 0.278 0.0284 0.0834
#> 4 rs7502 0.423 0.0455 1.17
#> 5 rs7892 0.101 0.0170 0.298
#> 6 rs9441 0.307 0.0739 1.83
#> 7 rs11071 0.123 0.0284 0.0143
#> 8 rs11183 0.458 0.0568 1.15
#> 9 rs11291 0.244 0.0455 0.391
#> 10 rs12971 0.312 0.0625 0.112
#> # ℹ 69 more rows