Summary of STOAT's results — summary

Print a few summary metrics from the association results

Usage

summary_stoat(assoc)

Arguments

assoc: Either the data.frame imported by *import_assoc*, or the path to STOAT's output (*assoc.pvalues.tsv.gz)

Value

In addition to printing the summary metrics, returns a list with the values

Examples

# prepare the filename
assoc_file = system.file('extdata/stoat.quantitative.assoc.pvalues.tsv.gz', package='StoatPlot')

# print a summary
sum.l = summary_stoat(assoc_file)
#> 
#> 
#> |Metric                   | Value|
#> |:------------------------|-----:|
#> |Total variants           |   680|
#> |Variant PV<0.01          |    31|
#> |Variant adjusted PV<0.01 |     2|
#> |Genomic inflation factor |  1.15|
#> 
#> 
#> |Type | Total| Pv_BH_below_0.01|
#> |:----|-----:|----------------:|
#> |SNP  |   519|                2|
#> |SV   |   161|                0|
#> 
#> 
sum.l 
#> $all
#> # A tibble: 4 × 2
#>   Metric                    Value
#>   <chr>                     <dbl>
#> 1 Total variants           680   
#> 2 Variant PV<0.01           31   
#> 3 Variant adjusted PV<0.01   2   
#> 4 Genomic inflation factor   1.15
#> 
#> $per.type
#> # A tibble: 2 × 3
#>   Type  Total Pv_BH_below_0.01
#>   <fct> <int>            <int>
#> 1 SNP     519                2
#> 2 SV      161                0
#>