Extracts variants from a VariantAnnotation VCF object — extract_variants_from

Aaron - Need to describe differnce between ID, and name in the header, and rename in terms of naming the sample. Need to describe differences in multiallelic choices. Also need to describe the automatic error fixing

Usage

extract_variants_from_vcf(
  vcf,
  id = NULL,
  rename = NULL,
  sample_field = NULL,
  filter = TRUE,
  multiallele = c("expand", "exclude"),
  extra_fields = NULL
)

Arguments

vcf: Location of vcf file
id: ID of the sample to select from VCF. If NULL, then the first sample will be selected. Default NULL.
rename: Rename the sample to this value when extracting variants. If NULL, then the sample will be named according to ID.
sample_field: Some algoriths will save the name of the sample in the ##SAMPLE portion of header in the VCF (e.g. ##SAMPLE=<ID=TUMOR,SampleName=TCGA-01-0001>). If the ID is specified via the id parameter ("TUMOR" in this example), then sample_field can be used to specify the name of the tag ("SampleName" in this example). Default NULL.
filter: Exclude variants that do not have a PASS in the FILTER column of the VCF. Default TRUE.
multiallele: Multialleles are when multiple alternative variants are listed in the same row in the vcf. One of "expand" or "exclude". If "expand" is selected, then each alternate allele will be given their own rows. If "exclude" is selected, then these rows will be removed. Default "expand".
extra_fields: Optionally extract additional fields from the INFO section of the VCF. Default NULL.

Value

Returns a data.table of variants from a vcf

Examples

vcf_file <- system.file("extdata", "public_LUAD_TCGA-97-7938.vcf",
  package = "musicatk"
)

library(VariantAnnotation)
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
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#> Attaching package: ‘matrixStats’
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#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> The following object is masked from ‘package:Biobase’:
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#> Attaching package: ‘VariantAnnotation’
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vcf <- readVcf(vcf_file)
variants <- extract_variants_from_vcf(vcf = vcf)