Transform DMR results to long format

Convert wide-format DMR results into a long-format table with explicit columns for contrasts, effect sizes, and significance values.

pivotDMRsLonger(DMRtable, FDRthres = 0.05, makePositive = FALSE)

Arguments

DMRtable

data.frame DMR results in wide format, typically produced by calculateDMRs().

FDRthres

numeric(1) False discovery rate threshold for filtering significant windows. Default: 0.05.

makePositive

logical(1) If TRUE, reverse the direction of contrasts so that all retained windows are positively associated with group1. Default: FALSE.

Value

A tibble:

• pivotDMRsLonger(): returns a long-format table with one row per DMR–contrast combination, including columns group1, group2, deltaBeta, log2FC, and adjPval.

See also

tidyr::pivot_longer(), summariseDMRsByContrast()

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

Examples

data(exampleTumourNormal, package = "mesa")

# Convert results to long format and filter at custom FDR threshold
exampleTumourNormal %>%
    calculateDMRs(
        variable = "type",
        contrasts = "LUAD_vs_NormalLung",
        FDRthres = 0.1
    ) %>%
    pivotDMRsLonger(FDRthres = 0.1)
#> Generating table of nrpm values for 819 regions across 5 samples.
#> Fitting initial GLM on 255 windows, without using parallelisation.
#> Performing contrast LUAD_vs_NormalLung
#> Contrasts Complete
#> selecting regions from contrast LUAD_vs_NormalLung
#> selected 58/255 windows
#> adding test results from LUAD_vs_NormalLung
#> # A tibble: 58 × 19
#>    seqnames    start      end CpG_density NormalColon_beta_means CRC_beta_means
#>    <fct>       <int>    <int>       <dbl>                  <dbl>          <dbl>
#>  1 7        25107301 25107600        8.13                 0.364          0.293 
#>  2 7        27096001 27096300       18.8                  0.0229         0.0259
#>  3 7        27096301 27096600       19.9                  0.0431         0.0133
#>  4 7        27096601 27096900       12.6                  0.0317         0.0187
#>  5 7        27096901 27097200       17.9                  0.0341         0.0136
#>  6 7        27098401 27098700       12.1                  0.203          0.484 
#>  7 7        27099001 27099300       13.1                  0.304          0.487 
#>  8 7        27103501 27103800       13.1                  0.247          0.686 
#>  9 7        27106501 27106800       19.0                  0.972          0.983 
#> 10 7        27106801 27107100       13.1                  0.859          0.958 
#> # ℹ 48 more rows
#> # ℹ 13 more variables: NormalLung_beta_means <dbl>, LUAD_beta_means <dbl>,
#> #   LUSC_beta_means <dbl>, NormalColon_nrpm_means <dbl>, CRC_nrpm_means <dbl>,
#> #   NormalLung_nrpm_means <dbl>, LUAD_nrpm_means <dbl>, LUSC_nrpm_means <dbl>,
#> #   group1 <chr>, group2 <chr>, log2FC <dbl>, adjPval <dbl>, deltaBeta <dbl>