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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
, orAlt
) you expect in the reference. Ex. for A to I editing events, this would beA
.- edit_to
This should correspond to a nucleotide or assay (
A
,C
,G
,T
,Ref
, orAlt
) you expect in the editing site. Ex. for A to I editing events, this would beG
.- 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
andmax_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