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
allele.info.WGS.GCcor(): Allele Information with GC-Bias Correction for WGS Data
allele.info.WGS(): ClrCNV: multicopy detection for WGS
allele.info.WGS3(): Allele Information for WGS Data (No GC Correction)
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
rCNV rCNV-package: rCNV: Detect Copy Number Variants from SNP Data
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