readIID: read individual ID

In plinkFile: 'PLINK' (and 'GCTA') File Helpers

read individual ID

Description

Generate individual ID automatically, or based on a fam file.

Usage

readIID(fam, opt = NULL)

Arguments

fam	prefix or name of a PLINK file, or data fram from a FAM file.
opt	option (def=1: the 2nd column in FAM file).

Details

The option (opt) can be:

• 1 = the iid column in FAM (default),

• 2 = formated as fid.iid,

• 0 = nothing

• -1 = numbering of individuals, decimal

• -2 = numbering of individuals, zero-padded fix-length decimal

• -3 = numbering of individuals, zero-padded fix-length hexedemical or, a vector of IDs to use.

Value

a vector of individual ID

Examples

pfx <- file.path(system.file("extdata", package="plinkFile"), "m20")
readIID(pfx,  1) # opt= 1: IID
readIID(pfx,  2) # opt= 2: FID.IID
readIID(pfx, -1) # opt=-1: number sequence
readIID(pfx, -2) # opt=-2: number sequence, fixed length, decimal
readIID(pfx, -3) # opt=-3: number sequence, fixed length, hexidemical

plinkFile documentation built on Nov. 24, 2023, 5:10 p.m.