VcfStack {GenomicFiles} | R Documentation

## VcfStack and RangedVcfStack Objects

### Description

The `VcfStack` class is a vector of related VCF files, for instance each file representing a separate chromosome. The class helps manage these files as a group. The `RangedVcfStack` class extends `VcfStack` by associating genomic ranges of interest to the collection of VCF files.

### Constructor

  `VcfStack(files=NULL, seqinfo=NULL, colData=NULL, index=TRUE, check=TRUE)` Creates a VcfStack object.

  `files`

    A VcfFilelist object. If a VcfFile or character vector is given a VcfFileList will be coerced. The character vector should be files paths pointing to VCF files. The character vector must be named, with names correspond to seqnames in each VCF file.

  `seqinfo`

    A Seqinfo object describing the levels genome and circularity of each sequence.

  `colData`

    An optional DataFrame describing each sample in the VcfStack. When present, row names must correspond to sample names in the VCF file.

  `index`

    A logical indicating if the vcf index files should be created.

  `check`

    A logical indicating if the check across samples should be performed

  `RangedVcfStack(vs=NULL, rowRanges=NULL)` Creates a RangedVcfStack object.

  `vs`

    A `VcfStack` object.

  `rowRanges`

    An optional GRanges object associating the genomic ranges of interest to the collection of VCF files. The seqnames of `rowRanges` are a subset of `seqnames(vs)`. If missing, a default is created from the `seqinfo` object of the provided `VcfStack`.

### Accessors

In the code below, `x` is a VcfStack or RangedVcfStack object.

dim(x)

  Get the number of files and samples in the `VcfStack` object.

colnames(x, do.NULL=TRUE, prefix="col")

  Get the sample names in the `VcfStack`.

rownames(x), do.NULL=TRUE, prefix="row")

  Get the names of the files in `VcfStack`.

dimnames(x))

  Get the names of samples and the names of files in `VcfStack`.

files(x, ...), files(x, ..., check=TRUE) <- value

  Get or set the files on `x`. `value` can be a named character() of file paths or a VcfFileList. The return value will be a VcfFileList.

seqinfo(x), seqinfo(x, new2old = NULL, pruning.mode = c("error", "coarse", "fine", "tidy")) <- value

  Get or set the seqinfo on `x`. See seqinfo<- for details on `new2old` and `pruning.mode`.

seqlevelsStyle(x) <- value

  Set the seqlevels according to the supplied style. File names and rowRanges will also be updated if applicable. See seqlevelsStyle<- for more details.

colData(x), colData(x, ...) <- value

  Get or set the `colData` on `x`. `value` is a DataFrame.

rowRanges(x), rowRanges(x, ...) <- value

  Get or set the `rowRanges` on `x`. `x` has to be a `RangedVcfStack` object. `value` is a GRanges.

### Methods

In the code below, `x` is a VcfStack or RangedVcfStack object. `i` is a GRanges object, character() vector of seqnames, numeric() vector, logical() vector, or can be missing. For a RangedVcfStack object, assay and readVcfStack will use the associated `rowRanges` object for `i`.

vcfFields(x)

  Returns a `CharacterList` of all available VCF fields, with names of `fixed`, `info`, `geno` and `samples` indicating the four categories. Each element is a character() vector of available VCF field names within each category.

assay(x, i, ..., BPPARAM=bpparam())

  Get matrix of genotype calls from the VCF files. See genotypeToSnpMatrix. Argument `i` specifies which files to read. `BPPARAM` is the argument to the bpmapply.

readVcfStack(x, i, j=colnames(x), param=ScanVcfParam())

  Get content of VCF files in the VcfStack. `i` indicates which files to read. `j` can be missing or a character() vector of sample names (see samples) present in the VCF files. `param` is a ScanVcfParam object. If `param` is used `i` and `j` are ignored.

show(object)

  Display abbreviated information about `VcfStack` or `RangedVcfStack` object.

### Subsetting

In the code below, `x` is a VcfStack or RangedVcfStack object.

x[i, j]

  Get elements from ranges `i` and samples `j` as a VcfStack or RangedVcfStack object. Note: for a `RangedVcfStack`, the `rowRanges` object will also be subset.

  `i` can be missing, a character() vector of seqnames, numeric() vector of indexes, logical() or `GRanges` object. When `i` is a `GRanges` object, `seqnames(i)` is then used to subset the files in the VcfStack.

  `j` can be missing, a character() vector of sample names, a numeric(), logical() vector.

### Helpers

getVCFPath(vs, chrtok)

  Deprecated. Use `files(vs)[chrtok]` instead.

paths1kg(chrtoks)

  Translate seqnames `chrtoks` to 1000 genomes genotype VCF urls.

### Author(s)

Lori Shepherd mailto:Lori.Shepherd@RoswellPark.org and Martin Morgan mailto:Martin.Morgan@RoswellPark.org

### See Also

VcfFile, VcfFileList.

### Examples

    ## ---------------------------------------------------------------------
    ## CONSTRUCTION
    ## ---------------------------------------------------------------------
    ## point to VCF files and add names corresponding to the sequence
    ## present in the file
    extdata <- system.file(package="GenomicFiles", "extdata")
    files <- dir(extdata, pattern="^CEUtrio.*bgz$", full=TRUE)
    names(files) <- sub(".*_([0-9XY]+).*", "\\1", basename(files))

    ## input data.frame describing the length of each sequence, coerce to
    ## 'Seqinfo' object
    seqinfo <- as(readRDS(file.path(extdata, "seqinfo.rds")), "Seqinfo")

    stack <- VcfStack(files, seqinfo)
    stack

    ## Use seqinfo from VCF files instead of explict value
    stack2 <- VcfStack(files)

    rstack <- RangedVcfStack(stack)
    gr <- GRanges(c("7:1-159138000", "X:1-155270560"))
    rstack2 <- RangedVcfStack(stack, gr)
    rstack2

    ## ---------------------------------------------------------------------
    ## ACCESSORS
    ## ---------------------------------------------------------------------
    dim(stack)
    colnames(stack)
    rownames(stack)
    dimnames(stack)
    head(files(stack))
    seqinfo(stack)
    colData(stack)

    ## ---------------------------------------------------------------------
    ## METHODS
    ## ---------------------------------------------------------------------
    readVcfStack(stack, i=GRanges("20:862167-62858306"))
    i <- GRanges(c("20:862167-62858306", "7:1-159138000"))
    readVcfStack(stack, i=i, j="NA12891")

    head(assay(stack, gr))
    head(assay(rstack2))

    seqlevels(stack2)
    rownames(stack2)
    seqlevelsStyle(stack2)
    seqlevelsStyle(stack2) <- "UCSC"
    seqlevelsStyle(stack2)
    seqlevels(stack2)
    rownames(stack2)
    vcfFields(stack2)

    ## ---------------------------------------------------------------------
    ## SUBSETTING
    ## ---------------------------------------------------------------------
    ## select rows 4, 5, 6 and samples 1, 2
    stack[4:6, 1:2]
    ## select rownames "7", "11" and sample "NA12891"
    stack[c("7", "11"), "NA12891"]
    stack[c("7", "11", "X"), 2:3]
    ## subset with GRanges
    stack[GRanges("20:862167-62858306")]

    rstack2[]
    rstack2[,1]

    ## ---------------------------------------------------------------------
    ## HELPERS
    ## ---------------------------------------------------------------------
    paths1kg(1:3)

[Package GenomicFiles version 1.28.0 Index]