| admixture | admixture - estimate admixture components using supervised... |
| callbyChrPlot | Dot plot of variant call counts (hom alt and het) by... |
| calltypePlot | Bar plot of variants (counts) |
| chunkData | chunkData is a private function to read in a chunk and... |
| computeTiTv | Private function to calc transition tranversion (titv) ratio |
| didSamplePass | Getter for VCFEvaluate class to check if Sample Passed.... |
| didSamplePassOverall | Getter for VCFEvaluate class to check if Sample Passed.... |
| genotypeQualityPlot | Histogram of genotype qualities |
| getCoefs | Private function to calc coefficients for admixture |
| getDescriptors | Return vector of long descriptions for variable names |
| getName | Getter for VCFQAReport class to return filename slot |
| getPlots | Getter for VCFQAReport class to return plots slot. |
| getResults | Getter for VCFQAReport class to return results. Return a... |
| getVR | getVr is a Getter. Returns vr slot. |
| goldCompare | Comparator to gold standard |
| GoldData-class | Declare class Gold to store information from Gold" (1000... |
| GoldDataFromGRanges | User Constructor for class. Used to associate the gold... |
| GoldDataParam | User Constructor for class |
| GoldDataParam-class | Declare class GoldDataParam which will store thresholds to... |
| hetGap | Gap between HETs by Chromosome |
| hetsMasked | Number hets in masked GRanges |
| homrefPlot | Dot plot of variant call counts (hom ref) by chromosome |
| meanGQ | Mean Genotype Quality (GQ) |
| myf | Private function to calc likelihood for admixture |
| numberCalls | Total Calls. This is the total number of calls in the file... |
| numberOfHets | Count Number of Hets |
| numberOfHomRefs | Count Number of Hom Ref |
| numberOfHomVars | Count Number of Hom Vars |
| percentHets | Percent of Hets as Total number of variants |
| percentInTarget | percent in target range read depth For 15 to 60 for 30x (50... |
| rareCompare | Comparator to rare variants. Rare is defined as 0.01 percent... |
| readDepth | Median read depth |
| readdepthPlot | Histogram of read depth by GT |
| ReadGoldData | User Constructor for class |
| ReadVCFData | User Constructor for class. Calls VCFData constructor:... |
| ReadVCFDataChunk | User Constructor for class. Calls VCFData constructor:... |
| readVcfGold | Private method for class. Read in Gold file - will read in... |
| reformatData | Take in the results from the population data and re-format it |
| titv | Transition transversion ratio in coding and non-coding |
| VCFData-class | Declare class Reads in VCF using readVCFAsVRanges |
| VCFEvaluate | Constructor for class. Calls constructor for class. Using... |
| VCFQAParam | User Constructor for class. Call limits are set as default... |
| VCFQAParam-class | Declare class VCFQAParam which will store thresholds to apply... |
| VCFQAReport-class | Declare class VCFQAReport which will evaluate a VCF stored as... |
| XHeterozygosity | Calculate X heterozygosity to determine Gender |
