parallel.qtlhot {qtlhot}

Code for parallelizing R/qtlhot.

Description

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.

Usage

## 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)

Arguments

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

Author(s)

Brian S Yandell and Elias Chaibub Neto

See Also

read.cross