seqUnitApply {SeqArray} | R Documentation

## Apply Function Over Variant Units

### Description

Applies a user-defined function to each variant unit.

### Usage

    seqUnitApply(gdsfile, units, var.name, FUN, as.is=c("none", "list", "unlist"),
        parallel=FALSE, ..., .bl_size=256L, .progress=FALSE, .useraw=FALSE,
        .padNA=TRUE, .tolist=FALSE, .envir=NULL)

### Arguments

`gdsfile` | a `SeqVarGDSClass` object
`units` | a list of units of selected variants, with S3 class `SeqUnitListClass`
`var.name` | the variable name(s), see details
`FUN` | the function to be applied
`as.is` | returned value: a list, an integer vector, etc; return nothing by default `as.is="none"`; `as.is` can be a `connection` object, or a GDS node `gdsn.class` object; if "unlist" is used, produces a vector which contains all the atomic components, via `unlist(..., recursive=FALSE)`
`parallel` | `FALSE` (serial processing), `TRUE` (multicore processing), numeric value or other value; `parallel` is passed to the argument `cl` in `seqParallel`, see `seqParallel` for more details.
`.bl_size` | chuck size, the increment for load balancing, 256 for units
`.progress` | if `TRUE`, show progress information
`.useraw` | `TRUE`, force to use RAW instead of INTEGER for genotypes and dosages; `FALSE`, use INTEGER; `NA`, use RAW instead of INTEGER if possible; for genotypes, 0xFF is missing value if RAW is used
`.padNA` | `TRUE`, pad a variable-length vector with NA if the number of data points for each variant is not greater than 1
`.tolist` | if `TRUE`, return a list of vectors instead of the structure `list(length, data)` for variable-length data
`.envir` | NULL, an environment object, or a list/data.frame
`...` | optional arguments to `FUN`

### Details

The variable name should be `"sample.id"`, `"variant.id"`, `"position"`, `"chromosome"`, `"allele"`, `"genotype"`, `"annotation/id"`, `"annotation/qual"`, `"annotation/filter"`, `"annotation/info/VARIABLE_NAME"`, or `"annotation/format/VARIABLE_NAME"`.

`"@genotype"`, `"annotation/info/@VARIABLE_NAME"` or `"annotation/format/@VARIABLE_NAME"` are used to obtain the index associated with these variables.

`"$dosage"` is also allowed for the dosages of reference allele (integer: 0, 1, 2 and NA for diploid genotypes).

`"$dosage_alt"` returns a RAW/INTEGER matrix for the dosages of alternative allele without distinguishing different alternative alleles.

`"$num_allele"` returns an integer vector with the numbers of distinct alleles.

`"$ref"` returns a character vector of reference alleles

`"$alt"` returns a character vector of alternative alleles (delimited by comma)

`"$chrom_pos"` returns characters with the combination of chromosome and position, e.g., "1:1272721". `"$chrom_pos_allele"` returns characters with the combination of chromosome, position and alleles, e.g., "1:1272721_A_G" (i.e., chr:position_REF_ALT).

`"$variant_index"` returns the indices of selected variants starting from 1, and `"$sample_index"` returns the indices of selected samples starting from 1.

### Value

A vector, a list of values or none.

### Author(s)

Xiuwen Zheng

### See Also

`seqUnitSlidingWindows`, `seqUnitFilterCond`

### Examples

    # open the GDS file
    gdsfile <- seqOpen(seqExampleFileName("gds"))

    # variant units via sliding windows
    units <- seqUnitSlidingWindows(gdsfile)

    v1 <- seqUnitApply(gdsfile, units, "genotype", function(x) dim(x)[3L],
        as.is="unlist", .progress=TRUE)
    v2 <- seqUnitApply(gdsfile, units, "genotype", function(x) dim(x)[3L],
        as.is="unlist", parallel=2, .progress=TRUE)

    all(v1 == lengths(units$index))
    all(v1 == v2)

    # call with an external R variable
    ext <- list(x=1:1348/10)
    v3 <- seqUnitApply(gdsfile, units, "$:x", function(x) x,
        as.is="list", .progress=TRUE, .envir=ext)
    head(units$index)
    head(v3)

    table(sapply(seq_along(units$index), function(i) all(units$index[[i]] == v3[[i]]*10)))
    # all TRUE

    # close the GDS file
    seqClose(gdsfile)

[Package SeqArray version 1.28.1 Index]