Add allele counts to a muscadet object

This function adds allele counts data to the omics of a muscadet object. The data frames in the allele_counts list are assigned to the allelic slots of omics.

Usage

addAlleleCounts(x, allele_counts)

Arguments

x

A muscadet object.

allele_counts

A list of data frames where each data frame contains allele counts for a specific omic (list). The list must have the same length and order as the number of omics in the x object. Each data frames must contain the following columns : cell, id, CHROM, POS, REF, ALT, RD, AD, DP, GT. See allele_counts for details.

Value

A modified muscadet object with updated allele counts in the allelic slot of each muscomic object in the omics slot.

Note

As the allele counts are not used for computing log R ratios and cell clustering, they are not mandatory at the creation of muscomic and muscadet objects. The allele counts data can be added to objects later with this addAlleleCounts function, before using the mergeCounts() function.

This function is also useful to add allele counts for individual-specific variant positions to a common muscadet object, for example for the reference muscadet object: a common muscadet object with reference coverage data can be stored as a unique object to use as reference for computing log R ratios for all samples, and then it can updated with allele counts at individual-specific variant positions (e.g. found by bulk sequencing) before Copy Number Alterations (CNAs) calling.

See also

CreateMuscomicObject(), mergeCounts()

Examples

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

# Add allele counts data frames to muscadet objects
muscadet_obj <- addAlleleCounts(
    muscadet_obj,
    allele_counts = list(allele_counts_atac_tumor, allele_counts_rna_tumor))
muscadet_obj_ref <- addAlleleCounts(
    muscadet_obj_ref,
    allele_counts = list(allele_counts_atac_ref, allele_counts_rna_ref))