GoldData-class
(Package: genotypeeval) :
Declare class Gold to store information from Gold" (1000 Genomes for example) along with the GoldDataParam
Declare class Gold to store information from Gold" (1000 Genomes for example) along with the GoldDataParam
● Data Source:
BioConductor
● Keywords:
● Alias: GoldData-class
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GoldDataFromGRanges
(Package: genotypeeval) :
User Constructor for class. Used to associate the gold params object with the gold granges and to check if MAF is present.
User Constructor for class. Used to associate the gold params object with the gold granges and to check if MAF is present.
● Data Source:
BioConductor
● Keywords:
● Alias: GoldDataFromGRanges
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GoldDataParam-class
(Package: genotypeeval) :
Declare class GoldDataParam which will store thresholds to apply to VCFEvaluate object. This is intended for use in batch mode when a large number of vcf files needs to be screened and individual vcf files that fail flagged.
Declare class GoldDataParam which will store thresholds to apply to VCFEvaluate object. This is intended for use in batch mode when a large number of vcf files needs to be screened and individual vcf files that fail flagged. All limits follow the format lower limit than upper limit
● Data Source:
BioConductor
● Keywords:
● Alias: GoldDataParam-class
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User Constructor for class
● Data Source:
BioConductor
● Keywords:
● Alias: GoldDataParam
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User Constructor for class
● Data Source:
BioConductor
● Keywords:
● Alias: ReadGoldData
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ReadVCFData
(Package: genotypeeval) :
User Constructor for class. Calls VCFData constructor:
User Constructor for class. Calls VCFData constructor: ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL chromosomes, and MULTI calls. It scans the header of the vcf file and adds in the following fields for analysis if present: AD, GT, DP, GQ. Looks for the "END" tag in the header and reads in file as gVCF if necessary.
● Data Source:
BioConductor
● Keywords:
● Alias: ReadVCFData
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ReadVCFDataChunk
(Package: genotypeeval) :
User Constructor for class. Calls VCFData constructor:
User Constructor for class. Calls VCFData constructor: ReadVCFDataChunk is a wrapper for readVcfAsVRanges. It removes indels, GL chromosomes, and MULTI calls. It scans the header of the vcf file and adds in the following fields for analysis if present: AD, GT, DP, GQ. Looks for the "END" tag in the header and reads in file as gVCF if necessary. This is a multi core version of readVCFData. Note, input file must have been zipped and have a corresponding tabix file. It will drop all hom ref sites not in the admixture file but retain the counts of homref and multi in the VCF file. This means that a few of the metrics and the hom ref plot can no longer be calculated in VCFQAReport. If the metrics can no longer be calculated, it will not be output. Please note that if using a filter on the data (eg gq.filter) this will not be applied to the hom ref and total number of calls. The filter is applied in the VCFQAReport step and the metrics number of hom ref and total number of calls is calculated while reading in the file. When calling this function keep in mind the memory requirements. For example, if numcores=6, then when submitting the job you may request 12 Gb each core (72 Gb total). However the VCF in memory will need to fit back onto a single core or else R will not be able to allocate the memory. The given example here does not make sense to run as it includes only chromosome 22.
● Data Source:
BioConductor
● Keywords:
● Alias: ReadVCFDataChunk
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Declare class Reads in VCF using readVCFAsVRanges
● Data Source:
BioConductor
● Keywords:
● Alias: VCFData-class
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VCFEvaluate
(Package: genotypeeval) :
Constructor for class. Calls constructor for class. Using the GENO fields present in the vcf header will evaluate the vcf file using metrics and generate plots. Each metric will be tested against the params specified in the params class. For example, if Read Depth is in the GENO header will calculate median read depth, percent in target (50 percent to 200 percent of the target specified in the params file) and generate a histogram of Read Depth.
Constructor for class. Calls constructor for class. Using the GENO fields present in the vcf header will evaluate the vcf file using metrics and generate plots. Each metric will be tested against the params specified in the params class. For example, if Read Depth is in the GENO header will calculate median read depth, percent in target (50 percent to 200 percent of the target specified in the params file) and generate a histogram of Read Depth.
● Data Source:
BioConductor
● Keywords:
● Alias: VCFEvaluate
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VCFQAParam-class
(Package: genotypeeval) :
Declare class VCFQAParam which will store thresholds to apply to VCFEvaluate object. This is intended for use in batch mode when a large number of vcf files needs to be screened and individual vcf files that fail flagged.
Declare class VCFQAParam which will store thresholds to apply to VCFEvaluate object. This is intended for use in batch mode when a large number of vcf files needs to be screened and individual vcf files that fail flagged. All limits follow the format lower limit than upper limit
● Data Source:
BioConductor
● Keywords:
● Alias: VCFQAParam-class
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