seqGetData: Get Data

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Get Data

Description

Gets data from a SeqArray GDS file.

Usage

seqGetData(gdsfile, var.name, .useraw=FALSE, .padNA=TRUE, .tolist=FALSE,
    .envir=NULL)

Arguments

gdsfile	a SeqVarGDSClass object
var.name	a variable name or a character vector, see details; if character(), return NULL
.useraw	TRUE, force to use RAW instead of INTEGER for genotypes and dosages; FALSE, use INTEGER; NA, use RAW for small numbers instead of INTEGER if possible; 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, a list or a data.frame

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).

"$dosage_alt" returns a RAW/INTEGER matrix for the dosages of alternative allele without distinguishing different alternative alleles. "$dosage_alt2" allow the alleles are partially missing (e.g., genotypes on chromosome X for males)

"$dosage_sp" returns a sparse matrix (dgCMatrix) for the dosages of alternative allele without distinguishing different alternative alleles. "$dosage_sp2" allow the alleles are partially missing (e.g., genotypes on chromosome X for males)

"$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_pos2" is similar to "$chrom_pos", except the suffix "_1" is added to the first duplicate following the variant, "_2" is added to the second duplicate, and so on. "$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.

"$:VAR" return the variable "VAR" from .envir according to the selected variants.

Value

Return vectors, matrices or lists (with length and data components) with a class name SeqVarDataList.

Author(s)

Xiuwen Zheng

See Also

seqSetFilter, seqApply, seqNewVarData, seqListVarData

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"))

# get 'chromosome'
table(seqGetData(f, "chromosome"))

# get 'allele'
head(seqGetData(f, "allele"))
# "T,C" "G,A" "G,A" ...

# get '$chrom_pos'
head(seqGetData(f, "$chrom_pos"))

# get '$dosage'
seqGetData(f, "$dosage")[1:6, 1:10]

# get a sparse matrix of dosages
seqGetData(f, "$dosage_sp")[1:6, 1:10]

# get '$num_allele'
head(seqGetData(f, "$num_allele"))


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

# get a list
seqGetData(f, c(chr="chromosome", pos="position", allele="allele"))

# get the indices of selected variants/samples
seqGetData(f, "$variant_index")
seqGetData(f, "$sample_index")

# get genotypic data
seqGetData(f, "genotype")

# get annotation/info/DP
seqGetData(f, "annotation/info/DP")

# get annotation/info/AA, a variable-length dataset
seqGetData(f, "annotation/info/AA", .padNA=FALSE)
# $length              <- indicating the length of each variable-length data
# [1] 1 1 1 1 1 1 ...
# $data                <- the data according to $length
# [1] "T" "C" "T" "C" "G" "C" ...

# or return a simplified vector
seqGetData(f, "annotation/info/AA", .padNA=TRUE)

# get annotation/format/DP, a variable-length dataset
seqGetData(f, "annotation/format/DP")
# $length              <- indicating the length of each variable-length data
# [1] 1 1 1 1 1 1 ...
# $data                <- the data according to $length
#      variant
# sample [,1] [,2] [,3] [,4] [,5] [,6] ...
#  [1,]   25   25   22    3    4   17  ...


# get values from R environment
env <- new.env()
env$x <- 1:1348 / 10
env$x[seqGetData(f, "$variant_index")]
seqGetData(f, "$:x", .envir=env)


# close the GDS file
seqClose(f)

zhengxwen/SeqArray documentation built on Dec. 14, 2024, 8:36 p.m.