plinkFile (version 0.2.1)

readVID: read variant ID

Description

Generate variant ID automatically, or based on a bim file.

Usage

readVID(bim, opt = NULL, vfr = NULL, vto = NULL)

Value

a vector of variant ID

Arguments

bim

prefix or name of a PLINK file, or data frame from a BIM file.

opt

option (def=1: the 2nd column in BIM file).

vfr

variant-wise, from where to read? (index/proportion, def=1).

vto

varinat-wise, to where then stop? (index/proportion, def=P).

Details

The option (opt) can be:

• 1 = the 2nd column in pfx.bim (default),

• 2 = formated as %CHR(02d):%BPS(09d),

• 3 = formated as %CHR(02d):%BPS(09d)_AL1(s)_AL2(s)

• 0 = nothing

• -1 = numbering of variants, decimal

• -2 = numbering of variants, zero-padded, fixed length decimal

• -3 = numbering of variants, zero-padded, fixed length hexedemical

• or, a vector of IDs to use.

Examples

# read variant ID
pfx <- file.path(system.file("extdata", package="plinkFile"), "m20")

# opt=1: 2nd column in the BED file (default)
vid <- readVID(pfx, 1); head(vid); tail(vid)

# opt=2: format by position
vid <- readVID(pfx, 2); head(vid); tail(vid)

# opt=3: format by position and alleles
vid <- readVID(pfx, 3); head(vid); tail(vid)

# opt=-1: number sequence
vid <- readVID(pfx, -1); head(vid); tail(vid)

# opt=-2: number sequence, fixed length, decimal
vid <- readVID(pfx, -2); head(vid); tail(vid)

# opt=-3: number sequence, fixed length, hexidemical
vid <- readVID(pfx, -3); head(vid); tail(vid)