Evaluating SNV-Induced Disruption of G-Quadruplex Structures

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Documentation for package ‘G4SNVHunter’ version 1.1.5

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

Help Pages

checkSNV	Check the validity of SNVs
exportG4	Export Predicted G4s to a File
exportMutG4	Export G4s and Associated Variant Information to File
filterSNVImpact	Filter SNV Impact GRanges Object Based on User-Defined Thresholds
filterVarImpact	Filter Variant Impact G4 Object Based on User-Defined Thresholds
G4HunterDetect	Detect G4 Sequences Using the G4Hunter Algorithm
G4HunterScore	Calculate the G4Hunter Score for a Given Sequence
G4VarImpact	Evaluate the Impact of Variants (SNVs, Indels, MNVs) on G4 Sequences
loadSequence	Load Genome Sequences
loadVariant	Load Small Variant Data from VCF or MAF Files
plotG4Info	Plot Basic Statistics of G4s Detected by the G4HunterDetect Function
plotImpactedG4	Sequence Logo of the G4 Sequence and Its Mutant Counterpart
plotImpactSeq	Visualize the variants in G4 sequence
plotSNVImpact	Plot the Impact of SNVs on G4Hunter Scores
plotVarImpact	Plot the Impact of Variants on G4 Formation
snp_gr	Single Nucleotide Polymorphisms GRanges Object
SNVImpactG4	Evaluate the Impact of SNVs on G4 Sequences
snv_gr	Single Nucleotide Variant GRanges Object