summarizeVariants-methods: Summarize variants by sample

In VariantAnnotation: Annotation of Genetic Variants

Description

Variants in a VCF file are overlapped with an annotation region and summarized by sample. Genotype information in the VCF is used to determine which samples express each variant.

Usage

## S4 method for signature 'TxDb,VCF,CodingVariants'
summarizeVariants(query, subject, mode, ...)
## S4 method for signature 'TxDb,VCF,FiveUTRVariants'
summarizeVariants(query, subject, mode, ...)
## S4 method for signature 'TxDb,VCF,ThreeUTRVariants'
summarizeVariants(query, subject, mode, ...)
## S4 method for signature 'TxDb,VCF,SpliceSiteVariants'
summarizeVariants(query, subject, mode, ...)
## S4 method for signature 'TxDb,VCF,IntronVariants'
summarizeVariants(query, subject, mode, ...)
## S4 method for signature 'TxDb,VCF,PromoterVariants'
summarizeVariants(query, subject, mode, ...)
## S4 method for signature 'GRangesList,VCF,VariantType'
summarizeVariants(query, subject, mode, ...)
## S4 method for signature 'GRangesList,VCF,function'
summarizeVariants(query, subject, mode, ...)

Arguments

query	A TxDb or GRangesList object that serves as the annotation. GFF files can be converted to TxDb objects with makeTxDbFromGFF() in the GenomicFeatures package.
subject	A VCF object containing the variants.
mode	mode can be a VariantType class or the name of a function. When mode is a VariantType class, counting is done with locateVariants and counts are summarized transcript-by-sample. Supported VariantType classes include CodingVariants, IntronVariants, FiveUTRVariants, ThreeUTRVariants, SpliceSiteVariants or PromoterVariants. AllVariants() and IntergenicVariants are not supported. See ?locateVariants for more detail on the variant classes. mode can also be the name of any counting function that outputs a Hits object. Variants will be summarized by the length of the GRangesList annotation (i.e., 'length-of-GRangesList'-by-sample).
...	Additional arguments passed to methods such as ignore.strand A logical indicating if strand should be igored when performing overlaps.

Details

summarizeVariants uses the genotype information in a VCF file to determine which samples are positive for each variant. Variants are overlapped with the annotation and the counts are summarized annotation-by-sample. If the annotation is a GRangesList of transcripts, the count matrix will be transcripts-by-sample. If the GRangesList is genes, the count matrix will be gene-by-sample.

• Counting with locateVariants() :

  Variant counts are always summarized transcript-by-sample. When query is a GRangesList, it must be compatible with the VariantType-class given as the mode argument. The list below specifies the appropriate GRangesList for each mode.

  CodingVariants :

  coding (CDS) by transcript

  IntronVariants :

  introns by transcript

  FiveUTRVariants :

  five prime UTR by transcript

  ThreeUTRVariants :

  three prime UTR by transcript

  SpliceSiteVariants :

  introns by transcript

  PromoterVariants :

  list of transcripts

  When query is a TxDb, the appropriate region-by-transcript GRangesList listed above is extracted internally and used as the annotation.

• Counting with a user-supplied function :

  subject must be a GRangesList and mode must be the name of a function. The count function must take 'query' and 'subject' arguments and return a Hits object. Counts are summarized by the outer list elements of the GRangesList.

Value

A RangedSummarizedExperiment object with count summaries in the assays slot. The rowRanges contains the annotation used for counting. Information in colData and metadata are taken from the VCF file.

Author(s)

Valerie Obenchain

See Also

readVcf, predictCoding, locateVariants

Examples

  library(TxDb.Hsapiens.UCSC.hg19.knownGene)
  txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene 

  ## Read variants from VCF.
  fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
  vcf <- readVcf(fl, "hg19")
  ## Rename seqlevels to match TxDb; confirm the match.
  seqlevels(vcf) <- paste0("chr", seqlevels(vcf)) 
  intersect(seqlevels(vcf), seqlevels(txdb))

  ## ----------------------------------------
  ## Counting with locateVariants()
  ## ----------------------------------------
  ## TxDb as the 'query'
  coding1 <- summarizeVariants(txdb, vcf, CodingVariants())
  colSums(assays(coding1)$counts)

  ## GRangesList as the 'query'
  cdsbytx <- cdsBy(txdb, "tx")
  coding2 <- summarizeVariants(cdsbytx, vcf, CodingVariants()) 

  stopifnot(identical(assays(coding1)$counts, assays(coding2)$counts))

  ## Promoter region variants summarized by transcript
  tx <- transcripts(txdb)
  txlst <- splitAsList(tx, seq_len(length(tx)))
  promoter <- summarizeVariants(txlst, vcf, 
                                PromoterVariants(upstream=100, downstream=10))
  colSums(assays(promoter)$counts)

  ## ----------------------------------------
  ## Counting with findOverlaps() 
  ## ----------------------------------------

  ## Summarize all variants by transcript
  allvariants <- summarizeVariants(txlst, vcf, findOverlaps)
  colSums(assays(allvariants)$counts)

VariantAnnotation documentation built on Nov. 8, 2020, 5:08 p.m.