plink_logistic: GWA (single variant logistic regression) with PLINK
In imbs-hl/imbs: Collection of functions used at the IMBS

Description Usage Arguments Details Value

GWA (single variant logistic regression) with PLINK

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plink_logistic(bfile, output.prefix, test, sex, beta, intercept, ...,
  bed.file = NULL, bim.file = NULL, fam.file = NULL,
  exec = "plink2", num.threads, memory)

`bfile`	[`string`] The basename of the binary PLINK files.
`output.prefix`	[`string`] The basename of the new binary PLINK files.
`test`	[`string`] Genetic model to use. Choices are 'genotypic', 'hethom', 'dominant', and 'recessive'. The 'genotypic' modifier adds an additive effect/dominance deviation 2df joint test (with two genotype-dependent variables in the regression, one with 0/1/2 coding and the second with 0/1/0 coding), while 'hethom' uses 0/0/1 and 0/1/0 coding instead. The 'dominant' and 'recessive' modifiers specify a model assuming full dominance or recessiveness, respectively, for the A1 allele.
`sex`	[`flag`] Include sex as covariate?
`beta`	[`flag`] Output regression coefficients instead of OR?
`intercept`	[`flag`] Include intercept in output?
`...`	[`character`] Additional arguments passed to PLINK call.
`bed.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`bim.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`fam.file`	[`string`] Alternative to `bfile` interface. Specify `bed`, `bim` and `fam` files individually.
`exec`	[`string`] Path of PLINK executable.
`num.threads`	[`int`] Number of CPUs usable by PLINK. Default is determined by SLURM environment variables and at least 1.
`memory`	[`int`] Memory for PLINK in Mb. Default is determined by minimum of SLURM environment variables `SLURM_MEM_PER_CPU` and `num.threads * SLURM_MEM_PER_NODE` and at least 5000.
`tmp.dir`	[`string`] Path where to save temporary files. If not set by user, defaults to `tempdir()`.