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Make summarized experiment object for differential editing analysis

Source: R/differential_editing.R
make_de_object.Rd

Generates a RangedSummarizedExperiment object for use with edgeR or DESeq2 . Will generate a counts assay with a matrix formatted with 2 columns per sample, representing the reference and editing allele counts.

Usage

make_de_object(
  rse,
  edit_from = "A",
  edit_to = "G",
  min_prop = 0,
  max_prop = 1,
  min_samples = 1
)

Arguments

rse

A RangedSummarizedExperiment object

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.

min_prop

The minimum required proportion of reads edited at a site. At least min_samples need to pass this to keep the site.

max_prop

The maximum allowable proportion of reads edited at a site. At least min_samples need to pass this to keep the site.

min_samples

The minimum number of samples passing the min_prop and max_prop cutoffs to keep a site.

Value

RangedSummarizedExperiment for use with edgeR or DESeq2. Contains a counts assay with a matrix formatted with 2 columns per sample (ref and alt counts).

Examples

library(SummarizedExperiment)
rse_adar_ifn <- mock_rse()
rse <- calc_edit_frequency(rse_adar_ifn)
#> ℹ 6 sites had no coverage for calculating editing
dse <- make_de_object(rse, min_samples = 1)
assay(dse, "counts")[1:5, ]
#>                 wt_ref adar1_ko_ref wt_alt adar1_ko_alt
#> site_SSR3_102_2      0            0      0            1
#> site_SSR3_125_2      0            0      1            0
#> site_SSR3_156_2      1            0      0            0
#> site_SSR3_176_2      8           16     16            0
#> site_SSR3_198_2     24           15      1            0
dse
#> class: RangedSummarizedExperiment 
#> dim: 68 4 
#> metadata(0):
#> assays(1): counts
#> rownames(68): site_SSR3_102_2 site_SSR3_125_2 ... site_DHFR_399_2
#>   site_DHFR_430_2
#> rowData names(4): REF rpbz vdb sor
#> colnames(4): wt_ref adar1_ko_ref wt_alt adar1_ko_alt
#> colData names(4): sample n_sites edit_idx count