Summarise DMRs by gene

Aggregate differentially methylated region (DMR) windows by gene annotation.

summariseDMRsByGene(DMRtable)

Arguments

DMRtable

data.frame or GRanges Annotated DMRs. Must include the columns ENSEMBL, SYMBOL, and GENENAME (typically added with annotateWindows()).

Value

A tibble:

• summariseDMRsByGene(): returns one row per gene, with counts of associated DMRs and any aggregated metadata.

See also

annotateWindows(), summariseDMRsByContrast()

Other DMR-helpers: pivotDMRsLonger(), summariseDMRsByContrast(), writeDMRsToBed(), writeDMRsToExcel()

Examples

data(exampleTumourNormal, package = "mesa")

# Summarise DMRs with explicit annotation databases
if (requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene", quietly = TRUE) &&
    requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
    exampleTumourNormal %>%
        calculateDMRs(variable = "tumour", contrasts = "all") %>%
        annotateWindows(
            TxDb = "TxDb.Hsapiens.UCSC.hg38.knownGene",
            annoDb = "org.Hs.eg.db"
        ) %>%
        summariseDMRsByGene()
}
#> Calculating 1 possible contrasts on the tumour column.
#> Generating table of nrpm values for 819 regions across 10 samples.
#> Fitting initial GLM on 309 windows, without using parallelisation.
#> Performing contrast Normal_vs_Tumour
#> Contrasts Complete
#> selecting regions from contrast Normal_vs_Tumour
#> selected 23/309 windows
#> adding test results from Normal_vs_Tumour
#> >> Using Genome: hg38 ...
#> >> Using Genome: hg38 ...
#> >> Using Genome: hg38 ...
#> 'select()' returned 1:1 mapping between keys and columns
#> # A tibble: 8 × 4
#>   ENSEMBL         SYMBOL       GENENAME                                        n
#>   <chr>           <chr>        <chr>                                       <int>
#> 1 ENSG00000233429 HOTAIRM1     HOXA transcript antisense RNA, myeloid-spe…     5
#> 2 NA              HOTTIP       HOXA distal transcript antisense RNA            5
#> 3 ENSG00000240990 HOXA11-AS    HOXA11 antisense RNA                            3
#> 4 ENSG00000253405 EVX1-AS      EVX1 antisense RNA                              3
#> 5 ENSG00000106038 EVX1         even-skipped homeobox 1                         2
#> 6 ENSG00000122592 HOXA7        homeobox A7                                     2
#> 7 ENSG00000254369 HOXA-AS3     HOXA cluster antisense RNA 3                    2
#> 8 ENSG00000257184 HOXA10-HOXA9 HOXA10-HOXA9 readthrough                        1