filterMTvars: sanitize PASSing mitochondrial variant calls to a moderate...
In trichelab/MTseeker: Bioconductor Tools for Human Mitochondrial Variant Analysis
Description
Usage
Arguments
Value
Examples
Description
FIXME: generalize this to mm10
Usage
1
filterMTvars(vars, fp = TRUE, NuMT = 0.03, covg = 20, depth = 2)
Arguments
vars
an MVRanges or MVRangesList (will be unlisted and relisted)
fp
use false positive filters? (TRUE: use Triska fpFilter)
NuMT
variants with VAF < this number will be presumed NuMTs (0.03)
covg
minimum median read coverage across chrM to be considered (20)
depth
minimum altDepth for a variant to be retained (2)
Value
a filtered set of variants
Examples
1
2
library(MTseekerData)
filterMTvars(RONKSvariants$RO_1)
trichelab/MTseeker documentation built on March 8, 2021, 6:20 p.m.
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Description Usage Arguments Value Examples
Description
FIXME: generalize this to mm10
Usage
1 | filterMTvars(vars, fp = TRUE, NuMT = 0.03, covg = 20, depth = 2)
|
Arguments
vars |
an MVRanges or MVRangesList (will be unlisted and relisted) |
fp |
use false positive filters? (TRUE: use Triska fpFilter) |
NuMT |
variants with VAF < this number will be presumed NuMTs (0.03) |
covg |
minimum median read coverage across chrM to be considered (20) |
depth |
minimum altDepth for a variant to be retained (2) |
Value
a filtered set of variants
Examples
1 2 | library(MTseekerData)
filterMTvars(RONKSvariants$RO_1)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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