parallel.qtlhot: Code for parallelizing R/qtlhot.
In qtlhot: Inference for QTL Hotspots

Description Usage Arguments Author(s) See Also

Code for parallelizing R/qtlhot. See installed parallel directory for proper use. There is apparently an S3 parallel method, so doc has to be as shown below, even though it is called as parallel.qtlhot.

## S3 method for class 'qtlhot'
parallel(x, data = 1, ..., dirpath = ".")
qtlhot.phase0(dirpath, init.seed = 92387475, len = rep(400,16), n.mar = 185, n.ind = 112,
   n.phe = 100, latent.eff = 0, res.var = 1, lod.thrs, ...)
big.phase0(dirpath, cross, trait.file, trait.matrix, droptrait.names = NULL,
   keeptrait.names = NULL, lod.thrs, sex = "Sex", trait.index,
   batch.effect = NULL, size.set = 250, offset = 0, subset.sex = NULL, verbose = TRUE)

`x`	phase of parallel processing (1,2,3)
`data`	index for parallel processing (1,2,...)
`...`	additional arguments passed along
`dirpath`	directory path as character string
`init.seed`	initial seed for pseudorandom number generation
`len`	vector of chromosome lengths for simulated map
`n.mar`	number of markers for simulated map
`n.ind`	number of individuals for simulated cross
`n.phe`	number of phenotypes for simulated phenotypes
`latent.eff`	size of latent effect
`res.var`	magnitude of residual variance
`lod.thrs`	vector of LOD thresholds to examine
`cross`	object of class `cross`
`trait.file`	character string name of trait file
`trait.matrix`	character string name of trait matrix
`droptrait.names`	vector of character strings for traits to drop (none if `NULL`)
`keeptrait.names`	vector of character strings for traits to keep (keep all if `NULL`)
`sex`	character string name of phenotype for sex
`trait.index`	vector of character strings for trait names
`batch.effect`	character string for batch effect (none if `NULL`)
`size.set`	maximum size of set of traits to scan at one time
`offset`	offset for name of trait RData files
`subset.sex`	string of sex to subset on (both sexes if `NULL`)
`verbose`	verbose output if `TRUE`