Create a wide table for ML/visualisation where rows are samples and columns are genomic windows, using one normalisation/measure.
makeTransposedTable(qseaSet, normMethod = "nrpm", ...)qseaSet.
A qseaSet object containing methylation-enriched sequencing data.
Default: none (must be supplied).
character(1).
Measure to extract. Common choices include "nrpm" or "beta".
Default: "nrpm".
tidyselect specification or character().
Optional columns from the sample table to append as additional features
(e.g., group, tumour or c("group","tumour")).
Default: none.
A tibble with one row per sample and one column per genomic window, plus any appended sample-level metadata.
Internally obtains a window × sample matrix for normMethod, transposes it
to sample × window, and (if requested) appends selected sample-table
columns. Window columns are typically named "chr:start-end". If
measure suffixes are present in column names, they may be cleaned to
bare sample/window names (see removeNormMethodSuffix()).
data(exampleTumourNormal, package = "mesa")
# NRPM features (sample × first few windows) with a group column appended
exampleTumourNormal %>%
makeTransposedTable(normMethod = "nrpm", group) %>%
dplyr::select(1:6) %>%
head()
#> obtaining raw values for 10 samples in 819 windows
#> deriving nrpm values...
#> creating table...
#> Joining with `by = join_by(sample_name)`
#> # A tibble: 6 × 6
#> sample_name group chr7_25002001_25002300 chr7_25005001_25005300
#> <chr> <chr> <dbl> <dbl>
#> 1 Colon1_N Colon1_N 0 0.263
#> 2 Colon1_T Colon1_T 0.131 0
#> 3 Colon2_N Colon2_N 0.246 0
#> 4 Colon2_T Colon2_T 0.178 0
#> 5 Lung1_N Lung1_N 0.125 0
#> 6 Lung1_T Lung1_T 0.184 0
#> # ℹ 2 more variables: chr7_25008601_25008900 <dbl>,
#> # chr7_25011301_25011600 <dbl>
# Beta features; inspect dimensions
exampleTumourNormal %>%
makeTransposedTable(normMethod = "beta") %>%
dim()
#> obtaining raw values for 10 samples in 819 windows
#> deriving beta values...
#> creating table...
#> Joining with `by = join_by(sample_name)`
#> [1] 10 820