seqUnitApply: Apply Function Over Variant Units
In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description Usage Arguments Details Value Author(s) See Also Examples

Applies a user-defined function to each variant unit.

1
2
3

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)

`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`

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.

A vector, a list of values or none.

Xiuwen Zheng

seqUnitSlidingWindows, seqUnitFilterCond

# 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)