Get counts per window

Convenience wrapper around getDataTable() to extract raw counts. Returns a window × sample (or group) table for downstream summaries/plots.

getCountTable(
  qseaSet,
  useGroupMeans = FALSE,
  addMethodSuffix = FALSE,
  verbose = TRUE
)

Arguments

qseaSet

qseaSet. A qseaSet object containing methylation-enriched sequencing data. Default: none (must be supplied).

useGroupMeans

logical(1). If TRUE, average replicates by the group column in the sample table and return group means; if FALSE, return per-sample counts. Default: FALSE.

addMethodSuffix

logical(1). If TRUE, keep the method suffix in column names (e.g., Sample1_counts or Group_counts_means); if FALSE, return bare sample/group names. Default: FALSE.

verbose

logical(1). Print progress/messages. Default: TRUE.

Value

A tibble/data.frame with one row per genomic window and columns for each sample (or group), plus any window metadata included by getDataTable().

See also

getDataTable(), getNRPMTable(), getBetaTable()

Other table-helpers: getBetaTable(), getDataTable(), getNRPMTable(), getSampleGroups2(), makeTransposedTable(), removeLibraryFactors(), removeNormMethodSuffix()

Examples

data(exampleTumourNormal, package = "mesa")

# Per-sample counts (first rows/columns)
exampleTumourNormal %>%
  getCountTable() %>%
  dplyr::select(1:6) %>%
  head()
#> Generating table of counts values for 819 regions across 10 samples.
#> # A tibble: 6 × 6
#>   seqnames    start      end CpG_density Colon1_N Colon1_T
#>   <fct>       <int>    <int>       <dbl>    <dbl>    <dbl>
#> 1 7        25002001 25002300        5.51        0        1
#> 2 7        25005001 25005300       13.4         1        0
#> 3 7        25008601 25008900        5.57        0        0
#> 4 7        25011301 25011600        5.10        0        1
#> 5 7        25017601 25017900        8.38        0        0
#> 6 7        25017901 25018200       17.9         0        4

# Group means instead of individual samples
exampleTumourNormal %>%
  getCountTable(useGroupMeans = TRUE) %>%
  dplyr::select(1:6) %>%
  head()
#> Generating table of counts values for 819 regions across 10 sample groups.
#> # A tibble: 6 × 6
#>   seqnames    start      end CpG_density Colon1_N Colon1_T
#>   <fct>       <int>    <int>       <dbl>    <dbl>    <dbl>
#> 1 7        25002001 25002300        5.51        0        1
#> 2 7        25005001 25005300       13.4         1        0
#> 3 7        25008601 25008900        5.57        0        0
#> 4 7        25011301 25011600        5.10        0        1
#> 5 7        25017601 25017900        8.38        0        0
#> 6 7        25017901 25018200       17.9         0        4

# Keep the method suffix in column names
exampleTumourNormal %>%
  getCountTable(addMethodSuffix = TRUE) %>%
  names() %>%
  head()
#> Generating table of counts values for 819 regions across 10 samples.
#> [1] "seqnames"        "start"           "end"             "CpG_density"    
#> [5] "Colon1_N_counts" "Colon1_T_counts"