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

Description Usage Arguments Details Value

Quality control on marker level with PLINK

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plink_marker_qc(bfile, output.prefix, call.rate, min.maf, max.maf,
  hwe.pval, mid.p = TRUE, ..., 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.
`call.rate`	[`double`] Filter out all variants with call rates falling below the provided threshold.
`min.maf`	[`double`] Filter out all variants with minor allele frequency below the provided threshold.
`max.maf`	[`double`] Filter out all variants with minor allele frequency above the provided threshold.
`hwe.pval`	[`double`] Filter out all variants which have Hardy-Weinberg equilibrium exact test p-value below the provided threshold.
`mid.p`	[`double`] Apply the mid-p adjustment? See Details.
`...`	[`character`] Additional arguments passed to PLINK.
`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.

The 'mid.p' modifier applies the mid-p adjustment described in Graffelman J, Moreno V (2013). The mid-p adjustment tends to bring the null rejection rate in line with the nominal p-value, and also reduces the filter's tendency to favor retention of variants with missing data. PLINK recommends its use. See PLINK manual https://www.cog-genomics.org/plink/1.9/.

Captured system output as character vector and number of markers excluded per criteria.

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