seqBlockApply {SeqArray} | R Documentation

## Apply Functions Over Array Margins via Blocking

### Description

Returns a vector or list of values obtained by applying a function to margins of genotypes and annotations via blocking.

### Usage

    seqBlockApply(gdsfile, var.name, FUN, margin=c("by.variant"),
        as.is=c("none", "list", "unlist"), var.index=c("none", "relative", "absolute"),
        bsize=1024L, parallel=FALSE, .useraw=FALSE, .padNA=TRUE, .tolist=FALSE,
        .progress=FALSE, ...)

### Arguments

`gdsfile` | a `SeqVarGDSClass` object
`var.name` | the variable name(s), see details
`FUN` | the function to be applied
`margin` | giving the dimension which the function will be applied over
`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)`
`var.index` | if `"none"` (by default), call `FUN(x, ...)` without variable index; if `"relative"` or `"absolute"`, add an argument to the user-defined function `FUN` like `FUN(index, x, ...)` where `index` is an index of variant starting from 1 if `margin = "by.variant"`: `"relative"` for indexing in the selection defined by `seqSetFilter`, `"absolute"` for indexing with respect to all data
`bsize` | block size
`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.
`.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
`.progress` | if `TRUE`, show progress information
`...` | 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.

The algorithm is highly optimized by blocking the computations to exploit the high-speed memory instead of disk.

### Value

A vector, a list of values or none.

### Author(s)

Xiuwen Zheng

### See Also

`seqApply`, `seqSetFilter`, `seqGetData`, `seqParallel`, `seqGetParallel`

### Examples

    # the GDS file
    (gds.fn <- seqExampleFileName("gds"))

    # display
    (f <- seqOpen(gds.fn))

    # get 'sample.id
    (samp.id <- seqGetData(f, "sample.id"))
    # "NA06984" "NA06985" "NA06986" ...

    # get 'variant.id'
    head(variant.id <- seqGetData(f, "variant.id"))

    # set sample and variant filters
    set.seed(100)
    seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10)],
        variant.id=sample(variant.id, 10))

    # read
    seqApply(f, "genotype", FUN=print, margin="by.variant")
    seqApply(f, "genotype", FUN=print, margin="by.variant", .useraw=TRUE)

    seqApply(f, "genotype", FUN=print, margin="by.sample")
    seqApply(f, "genotype", FUN=print, margin="by.sample", .useraw=TRUE)

    # read in block
    seqGetData(f, "$dosage")
    seqBlockApply(f, "$dosage", print, bsize=3)
    seqBlockApply(f, "$dosage", function(x) x, as.is="list", bsize=3)
    seqBlockApply(f, c(dos="$dosage", pos="position"), print, bsize=3)

    # close the GDS file
    seqClose(f)

[Package SeqArray version 1.28.1 Index]