getVariableLengthData: Get variable-length data
In SeqVarTools: Tools for variant data

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

Get data with multiple values per sample from a GDS object and return as an array

1 2	## S4 method for signature 'SeqVarGDSClass,character' getVariableLengthData(gdsobj, var.name, use.names=TRUE, parallel=FALSE)

`gdsobj`	A `SeqVarGDSClass` object with VCF data.
`var.name`	Character string with name of the variable, most likely "annotation/format/VARIABLE_NAME".
`use.names`	A logical indicating whether to assign sample and variant IDs as dimnames of the resulting matrix.
`parallel`	Logical, numeric, or other value to control parallel processing; see `seqParallel` for details.

Data which are indicated as having variable length (possibly different numbers of values for each variant) in the VCF header are stored as variable-length data in the GDS file. Each such data object has two components, "length" and "data." "length" indicates how many values there are for each variant, while "data" is a matrix with one row per sample and columns defined as all values for variant 1, followed by all values for variant 2, etc.

getVariableLengthData converts this format to a 3-dimensional array, where the length of the first dimension is the maximum number of values in "length," and the remaining dimensions are sample and variant. Missing values are given as NA. If the first dimension of this array would have length 1, the result is converted to a matrix.

An array with dimensions [n, sample, variant] where n is the maximum number of values possible for a given sample/variant cell. If n=1, a matrix with dimensions [sample,variant].

Stephanie Gogarten

SeqVarGDSClass, applyMethod, seqGetData

file <- system.file("extdata", "gl_chr1.gds", package="SeqVarTools")
gds <- seqOpen(file)
## genotype likelihood 
gl <- seqGetData(gds, "annotation/format/GL")
names(gl)
gl$length
## 3 values per variant - likelihood of RR,RA,AA genotypes
dim(gl$data)
## 85 samples (rows) and 9 variants with 3 values each - 27 columns

gl.array <- getVariableLengthData(gds, "annotation/format/GL")
dim(gl.array)
## 3 genotypes x 85 samples x 9 variants
head(gl.array[1,,])
head(gl.array[2,,])
head(gl.array[3,,])

seqClose(gds)