Convert qsea beta values to array-like probe matrix

Build a probe × sample beta table by mapping qseaSet windows to array probe coordinates. Currently supports Illumina Infinium 450k probes on GRCh38; a custom GRanges of probes can also be supplied.

convertToArrayBetaTable(qseaSet, arrayDetails = "Infinium450k")

Arguments

qseaSet

qseaSet. Input object providing per-window beta values. Default: none (must be supplied).

arrayDetails

character(1) or GRanges. Either a recognised keyword (currently "Infinium450k") or a GRanges of probe loci with an ID metadata column of probe identifiers. Coordinates must match the qseaSet genome (e.g., GRCh38). Default: "Infinium450k".

Value

A data.frame with one row per probe (including an ID column) and one column per sample containing the corresponding beta values. Probes with no matching/overlapping window receive NA.

Details

Probe coordinates are matched to qseaSet windows (e.g., via overlap). When multiple windows are relevant for a probe, the package's implementation is used to derive a single beta value per probe. Ensure the probe genome build matches the qseaSet (e.g., GRCh38) to avoid mismatches.

See also

getDataTable(), dataset mesa::hg38_450kArrayGR

Other window-helpers: calculateFractionReadsInGRanges(), downSample(), subsetWindowsBySignal(), subsetWindowsOverBackground()

Examples

data(exampleTumourNormal, package = "mesa")

# Use the built-in keyword for 450k probes (GRCh38)
exampleTumourNormal %>%
  convertToArrayBetaTable(arrayDetails = "Infinium450k") %>%
  head()
#> selecting specified ROIs
#> obtaining raw values for 10 samples in 724 windows
#> deriving beta values...
#> creating table...
#>           ID   Colon1_N   Colon1_T   Colon2_N   Colon2_T    Lung1_N   Lung1_T
#> 1 cg07628855 0.23631177 0.25657611 0.38851605 0.27410317 0.14973361 0.2473639
#> 2 cg20986166 0.23631177 0.25657611 0.38851605 0.27410317 0.14973361 0.2473639
#> 3 cg10626515 0.27941431 0.31468726 0.26731751 0.33483640 0.18763547        NA
#> 4 cg21433538 0.25522252 0.16195411 0.24284522 0.16033002 0.16554444 0.5702529
#> 5 cg14984920 0.07535972 0.04279569 0.07017123 0.04338794 0.04491717 0.1511983
#> 6 cg11496438 0.07535972 0.04279569 0.07017123 0.04338794 0.04491717 0.1511983
#>      Lung2_N    Lung2_T    Lung3_N    Lung3_T
#> 1 0.22838487 0.14690660 0.19599965 0.17212922
#> 2 0.22838487 0.14690660 0.19599965 0.17212922
#> 3 0.52722534 0.32436375 0.23822053 0.21263410
#> 4 0.13935910 0.16248322 0.21411349 0.18926005
#> 5 0.06908935 0.04410231 0.06068734 0.09997946
#> 6 0.06908935 0.04410231 0.06068734 0.09997946

# Supply an explicit GRanges of 450k probes (must have metadata column 'ID')
exampleTumourNormal %>%
  convertToArrayBetaTable(arrayDetails = mesa::hg38_450kArrayGR) %>%
  head()
#> selecting specified ROIs
#> obtaining raw values for 10 samples in 724 windows
#> deriving beta values...
#> creating table...
#>           ID   Colon1_N   Colon1_T   Colon2_N   Colon2_T    Lung1_N   Lung1_T
#> 1 cg07628855 0.23631177 0.25657611 0.38851605 0.27410317 0.14973361 0.2473639
#> 2 cg20986166 0.23631177 0.25657611 0.38851605 0.27410317 0.14973361 0.2473639
#> 3 cg10626515 0.27941431 0.31468726 0.26731751 0.33483640 0.18763547        NA
#> 4 cg21433538 0.25522252 0.16195411 0.24284522 0.16033002 0.16554444 0.5702529
#> 5 cg14984920 0.07535972 0.04279569 0.07017123 0.04338794 0.04491717 0.1511983
#> 6 cg11496438 0.07535972 0.04279569 0.07017123 0.04338794 0.04491717 0.1511983
#>      Lung2_N    Lung2_T    Lung3_N    Lung3_T
#> 1 0.22838487 0.14690660 0.19599965 0.17212922
#> 2 0.22838487 0.14690660 0.19599965 0.17212922
#> 3 0.52722534 0.32436375 0.23822053 0.21263410
#> 4 0.13935910 0.16248322 0.21411349 0.18926005
#> 5 0.06908935 0.04410231 0.06068734 0.09997946
#> 6 0.06908935 0.04410231 0.06068734 0.09997946