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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 duplicates
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