Calculate region methylation statistics

Calculate the average methylation probability and prevalence based on specified probability threshold.

Usage

region_methy_stats(nmr, regions, threshold = 0.5)

Arguments

nmr

the NanoMethResult object.

regions

the table of regions to query statistics for.

threshold

the threshold to use for determining methylation calls for the calculation of prevalence.

Value

table of regions with additional columns of methylation summary statistics.

Examples

nmr <- load_example_nanomethresult()
gene_anno <- exons_to_genes(NanoMethViz::exons(nmr))
region_methy_stats(nmr, gene_anno)
#> # A tibble: 6 × 8
#>   gene_id chr   strand symbol     start       end mean_methy_prob prevalence
#>   <chr>   <chr> <chr>  <chr>      <int>     <int>           <dbl>      <dbl>
#> 1 12189   chr11 -      Brca1  101488764 101551955           0.590      0.600
#> 2 12190   chr5  +      Brca2  150522630 150569747           0.557      0.565
#> 3 16210   chr18 +      Impact  12955852  12992950           0.586      0.594
#> 4 17263   chr12 +      Meg3   109541001 109571726           0.524      0.525
#> 5 18616   chr7  -      Peg3     6703892   6730431           0.618      0.628
#> 6 213742  chrX  -      Xist   103460366 103483254           0.520      0.519