plink_fst: Fst with PLINK
In imbs-hl/imbs: Collection of functions used at the IMBS

Description Usage Arguments Details Value

Fst with PLINK

plink_fst(bfile, output.prefix, pop.file, all.comb = TRUE,
  with.na = FALSE, outlier.removal = FALSE, outlier.sigma,
  num.outlier.evec, num.outlier.iter, ld.pruning.params, bed.file = NULL,
  bim.file = NULL, fam.file = NULL, exec = "plink2",
  tmp.dir = NULL, num.threads, memory)

`bfile`	[`string`] The basename of the binary PLINK files.
`output.prefix`	[`string`] The basename of the new binary PLINK files.
`pop.file`	[`string`] File defining disjoint clusters/strata of samples. FIDs in the first column, IIDs in the second column, and cluster names in the third column.
`all.comb`	[`flag`] Indicate if all population combinations should be considered for Fst calculation.
`with.na`	[`flag`] Indicate if samples with missing population identifier ('NA') should be considered as a valid population.
`outlier.removal`	[`flag`] Indicate if outliers shall be removed before final PCA computation.
`outlier.sigma`	[`int`] How many standard deviations from the mean of a single PC is not an outlier?
`num.outlier.evec`	[`int`] How many PCs shall be used for outlier detection?
`num.outlier.iter`	[`int`] Number of outlier iterations.
`ld.pruning.params`	[`list`] List with function arguments passed to `plink_ld_pruning`.
`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.
`tmp.dir`	[`string`] Path where to save temporary files. If not set by user, defaults to `tempdir()`.
`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.

First independent SNPs are extracted using PLINK LD pruning (plink_ld_pruning). If requested, outliers are detected and removed by calculating a PCA, calculating the mean (\hat{μ}_{j}) and standard deviation (\hat{σ}_{j}) of each principal component, and excluding those samples who's PC value v_{j} exceeds \hat{μ}_{j}\pmν\,\hat{σ}_{j} for at least one j, where ν is outlier.sigma.

A list of logs, Eigenvectors and Eigenvalues of the outlier removal and the final Fst values.

imbs-hl/imbs documentation built on Sept. 6, 2019, 11:05 p.m.