Summarize per-position modification frequency from modkit extract

Read a mod_calls.tsv.gz file from modkit extract and compute per-position modification frequency (proportion of reads with a non-canonical call code).

Usage

summarize_mod_calls(path, refs = NULL, min_reads = 1)

Arguments

path

Path to a mod_calls.tsv.gz file.

refs

Optional character vector of reference names to include.

min_reads

Minimum number of reads at a position to retain. Default 1.

Value

A tibble with columns: ref, pos, n_reads, n_mod, mod_freq.

Examples

path <- clover_example("ecoli/mod_calls.tsv.gz")
summarize_mod_calls(path)
#> # A tibble: 3 × 5
#>   ref                     pos n_reads n_mod mod_freq
#>   <chr>                 <dbl>   <int> <int>    <dbl>
#> 1 host-tRNA-Glu-TTC-1-1    34      15     3      0.2
#> 2 host-tRNA-Glu-TTC-1-1    46      15     3      0.2
#> 3 host-tRNA-Glu-TTC-1-1    55      15     0      0