Detecting Uniparental Disomy through NGS trio data

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Documentation for package ‘UPDhmm’ version 1.6.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addOr	Function to transform a large collapsed VCF into a dataframe, incorporating predicted states along with the log-likelihood ratio and p-value.
addRatioDepth	Add depth ratios (inside vs outside events) per sample
applyViterbi	Apply the hidden Markov model using the Viterbi algorithm.
asDfVcf	Function to transform a large collapsed VCF into a dataframe with predicted states, including chromosome, start position, end position and metadata.
blocksVcf	Function to simplify contiguous variants with the same state into blocks.
calculateEvents	Calculate UPD events in trio VCFs.
collapseEvents	Collapse events per sample and chromosome
hmm	HMM data for predicting UPD events in trio genomic data
identifyRecurrentRegions	Identify recurrent genomic regions across samples
markRecurrentRegions	Annotate regions as recurrent or non-recurrent
processChromosome	Process a single chromosome for UPD detection
vcfCheck	Check quality parameters (optional) and change IDs.