CalculateConsensus

We calculate the consensus information from the MAEGATK results. We set cells that have only alternative reads to 2 (Alternative). We set cells that have only reference reads to 1 (Reference). We set cells that have a mixture of alternative and reference reads to 3 (Both). We set cells that have no reads to 0 (NoCall).

Please note. Cells can have reads for the reference of a specific variant and no reads for the alternative. The cell can still have a reads for the other alternative alleles. Then the cell is still considered as 0 (NoCall) for this variant. For example: A cell has at position 3: 0 A reads, 53 T reads, 63 C reads, 148 T reads. For the variant chrM_3_T_A, the cell would have 53 reference reads, but also reads for other variants at this position. To make sure that there is no confusion, the cell is set to NoCall.

Usage

CalculateConsensus(SE, chromosome_prefix = "chrM", verbose = FALSE)

Arguments

SE

SummarizedExperiment object.

chromosome_prefix

The chromosome name used as a prefix.

verbose

Should the function be verbose? Default = FALSE