Package index • rCNV

All functions

ADnorm: Normalized allele depth example data

ADtable: Allele Depth (AD) example data

ad.correct(): Correct allele depth values

allele.freq(): Generate allele frequency table for individuals or populations

allele.info(): Get allele information for duplicate detection

alleleINF: Allele info example data

cnv(): Find CNVs from deviants

cpm.normal(): Calculate normalized depth for alleles

depthVsSample(): Simulate median allele ratios for varying number of samples and depth values

dup.plot(): Plot classified SNPs into deviants/CNVs and non-deviants/non-CNVs

dup.validate(): Validate detected deviants/cnvs

dupGet(): Detect deviants from SNPs; classify SNPs

exportVCF(): Export VCF files

get.miss(): Get missingness of individuals in raw vcf

gt.format(): Format genotype for BayEnv and BayPass

h.zygosity(): Determine per sample heterozygosity and inbreeding coefficient

hetTgen(): Generate allele depth or genotype table

maf(): Remove MAF allele

norm.fact(): Calculate normalization factor for each sample

power.bias(): Simulate and plot detection power of bias in allele ratios

readVCF(): Import VCF file

relatedness(): Determine pairwise relatedness

sig.hets(): Identify significantly different heterozygotes from SNPs data

sim.als(): Simulate Allele Frequencies

vcf.stat(): Get sequencing quality statistics of raw VCF files (with GatK generated vcf files only)

vst(): Calculate population-wise Vst

vstPermutation(): Run permutation on Vst