Merge a list of qseaSet objects (or .rds files containing them) into a
single qseaSet. Useful when cohorts were processed separately (e.g.,
tumour/normal, multiple runs) and need to be combined into one container.
combineQsetsList(
qseaSets,
firstQset = NULL,
dropDuplicates = TRUE,
checkParams = TRUE,
regionsToKeep = NULL
)list
List of qseaSet objects, or character() paths to .rds files containing
qseaSet objects. Default: none (must be supplied).
qseaSet or character(1)
Optional initial qseaSet to merge into. If a character(1) ending in
.rds, it is loaded via readr::read_rds().
Default: NULL.
logical(1)
If TRUE, drop samples with duplicated names across inputs. If FALSE,
duplicates are renamed by appending "_Dup".
Default: TRUE.
logical(1)
Verify that global parameters are identical across inputs.
Default: TRUE.
GRanges or coercible
If supplied, restrict each qseaSet to these genomic regions before
combining (saves memory). Accepts GRanges or a data frame with seqnames,
start, end.
Default: NULL (keep all regions).
A qseaSet object:
Combined samples from all inputs (or from firstQset plus inputs).
Duplicates handled according to dropDuplicates.
Regions optionally prefiltered by regionsToKeep prior to merge.
combineQsets() for pairwise merging.
data(exampleTumourNormal, package = "mesa")
# Split a cohort into Tumour and Normal, create a list, then combine back
tumours <- exampleTumourNormal %>% filter(tumour == "Tumour")
normals <- exampleTumourNormal %>% filter(tumour == "Normal")
qsetList <- list(tumours, normals)
combineQsetsList(qsetList)
#> No initial qseaSet given, using first element as initial qseaSet
#> Joining with `by = join_by(seqnames, start, end, width, strand, CpG_density)`
#> qseaSet
#> =======================================
#> 10 Samples:
#> Colon1_T, Colon2_T, Lung1_T, Lung2_T, Lung3_T, Colon1_N, Colon2_N, Lung1_N, Lung2_N, Lung3_N
#> 819 Regions in 22 chromosomes of BSgenome.Hsapiens.NCBI.GRCh38