getHeterozygosityBySample: Compute heterozygosity by sample
In bahlolab/moimix: Estimating mulitplicity of infection from high-throughput sequencing data
Description
Usage
Arguments
Details
Value
View source: R/seqarray_process_popgen.R
Description
Compute heterozygosity by sample
Usage
1
getHeterozygosityBySample(gdsfile)
Arguments
gdsfile
a SeqVarGDSClass object
Details
Follows the method outlined in Manske et al. 2012. Briefly,
for each sample, the reference and and alternate allele frequencies are computed
as the proportion of reads covering each allele. Then heterozygosity at a SNP
is 1 - (raf^2 + aaf^2)
Value
a numeric matrix of size l by n where l is the number of samples
and n is the number of SNPs.
bahlolab/moimix documentation built on April 16, 2020, 8:40 a.m.
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Description Usage Arguments Details Value
View source: R/seqarray_process_popgen.R
Description
Compute heterozygosity by sample
Usage
1 | getHeterozygosityBySample(gdsfile)
|
Arguments
gdsfile |
a |
Details
Follows the method outlined in Manske et al. 2012. Briefly, for each sample, the reference and and alternate allele frequencies are computed as the proportion of reads covering each allele. Then heterozygosity at a SNP is 1 - (raf^2 + aaf^2)
Value
a numeric matrix of size l by n where l is the number of samples and n is the number of SNPs.
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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