Merge counts for muscadet objects

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.

Usage

mergeCounts(x, reference, nor.het = TRUE)

Arguments

x

A muscadet object containing sample data (muscadet). This object must include clustering assignments in the cnacalling$clusters slot.

reference

A muscadet object 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 heterozygous positions are retrieve based on matched bulk sequencing data, and are thereby assumed to be heterozygous) before combining coverage and allelic data. Default is TRUE.

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

• omic = omic specific (omic column)

• all = for all omics

Examples

# Load example muscadet objects
data(muscadet_obj)
data(muscadet_obj_ref)

# Merge counts from all omics from both sample and reference
muscadet_obj <- mergeCounts(muscadet_obj, muscadet_obj_ref)