Adds editing frequencies — calc_edit

Adds editing frequencies to an existing RangedSummarizedExperiment object (created by pileup_sites()). The RangedSummarizedExperiment with a new assay for editing frequencies for each site (edit_freq), depth of coverage computed using the indicated edited nucleotides (depth) and new colData columns with the number of edited sites (n_sites) and the fraction of edits (edit_idx) is returned.

Usage

calc_edit_frequency(
  rse,
  edit_from = "A",
  edit_to = "G",
  drop = FALSE,
  replace_na = TRUE,
  edit_frequency = 0,
  min_count = 1
)

Arguments

rse: A RangedSummarizedExperiment object created by pileup_sites()
edit_from: This should correspond to a nucleotide or assay (A, C, G, T, Ref, or Alt) you expect in the reference. Ex. for A to I editing events, this would be A.
edit_to: This should correspond to a nucleotide or assay (A, C, G, T, Ref, or Alt) you expect in the editing site. Ex. for A to I editing events, this would be G.
drop: If TRUE, the RangedSummarizedExperiment returned will only retain sites matching the specified edit_from and edit_to bases.
replace_na: If TRUE, NA and NaN editing frequencies will be coerced to 0.
edit_frequency: The edit frequency cutoff used when calculating the number of sites. Set to 0 to require any non-zero editing frequency. The number of sites is stored as n_sites in the colData.
min_count: The minimum number of reads required when enumerating number of editing sites detected.

Value

RangedSummarizedExperiment supplemented with edit_freq and depth assay.

Examples

library(SummarizedExperiment)
rse_adar_ifn <- mock_rse()
rse <- calc_edit_frequency(rse_adar_ifn)
#> ℹ 6 sites had no coverage for calculating editing
assay(rse, "edit_freq")[1:5, ]
#>                        wt adar1_ko
#> site_SSR3_102_2 0.0000000        1
#> site_SSR3_125_2 1.0000000        0
#> site_SSR3_156_2 0.0000000        0
#> site_SSR3_176_2 0.6666667        0
#> site_SSR3_198_2 0.0400000        0