seqInfoNewVar: Add a variable to the INFO field

Description

Add a new variable to the INFO field in the specified GDS file.

Usage

seqInfoNewVar(gdsfile, var.name, variant.id, val, description="", compress=c("ZIP.MAX", ""), no.data.index=TRUE)

Arguments

gdsfile

a SeqVarGDSClass object

var.name

the variable name(s), see details

variant.id

the variant ID(s), should have the same order as IDs in the GDS file

val

a vector or a matrix with the same order as variant.id; if it is a matrix, the number of columns should be equal to the length of variant.id, see details

description

the variable description

compress

to specify the compression algorithm: "" for no compression; see compress in the function add.gdsn

no.data.index

applicable only if val is a numeric vector or a factor variable; if no.data.index=TRUE, non-exist values in val will be replaced by NA or NaN with respect to the variants not specified in variant.id, and no index data associated with this variable are created

Value

None.

Details

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

The argument val should be integers, numeric values, a logical variable, characters or factors. If val is a logical variable, one-bit storage mode will be used to store this variable, which corresponds to the variable defined with 'Type=Flag' in the VCF format.

Examples

Run this code

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

file.copy(gds.fn, "test.gds", overwrite=TRUE)

# display
(f <- seqOpen("test.gds", readonly=FALSE))

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


####    add variables to the INFO field    ####

set.seed(100)

seqInfoNewVar(f, "int", variant.id[1:15], sample.int(256, 15, TRUE),
	"integer variable")
seqGetData(f, "annotation/info/int")

seqInfoNewVar(f, "int.2", variant.id[1:15], sample.int(256, 15, TRUE),
	"integer variable", no.data.index=FALSE)
seqGetData(f, "annotation/info/int.2")


seqInfoNewVar(f, "numeric", variant.id[15:30], rnorm(16),
	"numeric variable")
seqGetData(f, "annotation/info/numeric")

seqInfoNewVar(f, "numeric.2", variant.id[15:30], rnorm(16),
	"numeric variable", no.data.index=FALSE)
seqGetData(f, "annotation/info/numeric.2")


seqInfoNewVar(f, "flag", variant.id[4:9], rep(c(FALSE, TRUE), 3),
	"flag variable")
# stored in `bit1'
seqGetData(f, "annotation/info/flag")


seqInfoNewVar(f, "factor", variant.id,
	factor(c("ABC", "DDD", "CVX")[sample(1:3, length(variant.id), TRUE)]),
	"string/factor variable")
# stored in `int32' with attributes
seqGetData(f, "annotation/info/factor")


seqInfoNewVar(f, "string", variant.id,
	c("ABC", "DDD", "CVX")[sample(1:3, length(variant.id), TRUE)],
	"string variable")
seqGetData(f, "annotation/info/string")


# show the file
f


# the corresponding VCF file
seqGDS2VCF(f, "test.vcf.gz")
txt <- strsplit(readLines("test.vcf.gz", n=40), "\t")[-c(1:21)]

# the INFO field:
sapply(txt, function(x) x[8])


# close the GDS file
seqClose(f)


# delete the temporary files
unlink("test.gds", force=TRUE)
unlink("test.vcf.gz", force=TRUE)