This function combines allelic (counts at variant positions, either common
SNPs or individual-specific heterozygous positions) and coverage counts
(counts on features) from all omics per cluster for both sample and
reference. The resulting merged data is stored in the cnacalling slot of
the sample muscadet object.
Arguments
- x
A
muscadetobject containing sample data (muscadet). This object must include clustering assignments in thecnacalling$clustersslot.- reference
A
muscadetobject containing reference data (muscadet).- nor.het
A logical value to specify if normal reference allele counts are modified to: total normal depth counts divided by 2, to force these positions to be heterozygous in the normal reference in allelic data (e.g. when reference cells are from a different individual but individual-specific heterozygous positions based on matched bulk sequencing data are used and thereby assumed to be heterozygous) before combining coverage and allelic data. Default is
TRUE.- quiet
Logical. If
TRUE, suppresses informative messages during execution. Default isFALSE.
Value
A modified muscadet object corresponding to the x
muscadet object, with updated cnacalling slot containing:
allelic.counts: Processed allelic counts on variant positions, for all omics.coverage.counts: Processed coverage counts merged with the reference.combined.counts: Combined data for allelic and coverage counts.
Abbreviations:
RD = Reference allele read depth
AD = Alternative allele read depth
DP = Total read depth
TUM = tumor sample
NOR = normal reference
Examples
# Load example muscadet object
# data("exdata_muscadet")
# data("exdata_muscadet_ref")
# Aggregate counts from all omics from both sample and reference
exdata_muscadet <- aggregateCounts(exdata_muscadet, exdata_muscadet_ref)
#> Clusters used: 1 (41 cells), 2 (36 cells)
#> Allelic data processing...
#> Coverage data processing...
#> Combining allelic and coverage data...