prepareComputePlan: Return a suitable compute plan for a genome-wide association study

Description

Instead of using OpenMx's default model processing sequence (i.e., omxDefaultComputePlan), it is more efficient and convienient to assemble a compute plan tailored for a genome-wide association study. This function returns a compute plan that loads SNP data into model modelName, fits the model, outputs the results to out, and repeats this procedure for all SNPs.

Usage

prepareComputePlan(model, snpData, out = "out.log", ..., SNP = NULL,
  startFrom = 1L)

Arguments

model

an instance of MxModel

snpData

the name of the file where the SNP data is stored

out

the filename where the results of fitted models shall be written

...

Not used. Forces remaining arguments to be specified by name.

SNP

a vector of SNP indices to include in the analysis; NULL is interpreted as all available SNPs

startFrom

the index to start from when SNP=NULL

Value

The given model with an appropriate compute plan.

Details

You can request a specific list of SNPs using the SNP argument. The numbers provided in SNP refer to offsets in the snpData file. For example, SNP=c(100,200) will process the 100th and 200th SNP. The first SNP in the snpData file is at offset 1. When SNP is omitted then all available SNPs are processed.

The suffix of snpData filename is interpreted to signal the format of how the SNP data is stored on disk. Suffixes ‘pgen’, ‘bed’, and ‘bgen’ are supported. Per-SNP descriptions are found in different places depending on the suffix. For ‘bgen’, both the SNP data and description are built into the same file. In the case of ‘pgen’, an associated file with suffix ‘pvar’ is expected to exist (see the spec for details). In the case of ‘bed’, an associated ‘bim’ file is expected to exist (see the spec for details). The chromosome, base-pair coordinate, and variant ID are added to each line of out.

A compute plan does not do anything by itself. You'll need to combine the compute plan with a model (such as returned by buildOneFac) to perform a GWAS.

Examples

Run this code

# NOT RUN {
m1 <- mxModel("test", mxFitFunctionWLS())
dir <- system.file("extdata", package = "gwsem")
m1 <- prepareComputePlan(m1, file.path(dir,"example.pgen"))
m1$compute
# }