plink_sample_qc: Quality control on sample level with PLINK
In imbs-hl/imbs: Collection of functions used at the IMBS

Description Usage Arguments Details Value

Quality control on sample level with PLINK

plink_sample_qc(bfile, output.prefix, call.rate, het.sigma,
  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.
`call.rate`	[`double`] Filter out all samples with call rates falling below the provided threshold.
`het.sigma`	[`double`] Filter out all samples with mean heterozygosity rate above or below `het.sigma` times estimated heterozygosity standard deviation.
`ld.pruning.params`	[`list`] List with function arguments passed to `plink_ld_pruning`.
`...`	[`character`] Additional arguments passed to ALL PLINK calls (LD pruning, heterozygosity estimation, exclusion of samples).
`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.

Heterozygosity estimation is not LD-sensitive, thus LD pruning is performend first using plink_ld_pruning. Heterozygosity estimate is based on SNPs only. See PLINK manual https://www.cog-genomics.org/plink/1.9/.

Captured system outputs as list of character vectors and number of samples excluded per criteria.

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