baseCountsFromBamList {mitoClone2} | R Documentation |
Uses the deepSNV
package to count nucleotide frequencies at
every position in the mitochondrial genome for every cell.
baseCountsFromBamList( bamfiles, sites = "chrM:1-16569", ncores = 1, ignore_nonstandard = FALSE )
bamfiles |
A character vector specifying the bam file paths |
sites |
String specifying genomic regions, defaults to the entire mitochondrial genome |
ncores |
Number of threads to use for the computation. Default 1 |
ignore_nonstandard |
Ignore basecalls that are not AGCTN |
A list of base count matrices which can serve as an input to
mutationCallsFromExclusionlist
or
mutationCallsFromCohort
bamCounts <- baseCountsFromBamList(bamfiles = list(system.file("extdata", "mm10_10x.bam", package="mitoClone2")),sites="chrM:1-15000", ncores=1)