callMT: call mitochondrial variants from the results of...

In RamsinghLab/ATACseeker: Utilities for ATACseq QC, differential accessibility, and integration

Description

call mitochondrial variants against the reference sequence they aligned to the appropriate cutoffs will depend on the estimated copy number of mtDNA in the cell type assayed; leukocytes usually have between 100-500, while hepatocytes can have thousands. Therefore different settings make sense for different cell types. The defaults call a mutation with ~ 2

Usage

callMT(mtReads, p.lower = 0.1, p.error = 0.001, read.count = 2L, ...)

Arguments

mtReads	mitochondrial reads, with bamViews, or a BAM filename
p.lower	lower bound on binomial probability for a variant (0.1)
p.error	error probability (influences the minimum VAF; 0.001)
read.count	minimum read depth required to support a variant (2)
...	any other arguments to pass (currently ignored)

RamsinghLab/ATACseeker documentation built on May 8, 2019, 8:05 a.m.