regainParallel: Parallel execution of the regression genetic association...

In insilico/npdro: Nearest-neighbor Projected-Distance Regression Optimized

Parallel execution of the regression genetic association interaction network (reGAIN) algorithm.

Description

regainParallel

Usage

regainParallel(
  depVarName = "class",
  labelledDataFrame,
  stdBetas = FALSE,
  absBetas = FALSE,
  numCores = 2,
  verbose = FALSE,
  writeBetas = FALSE,
  interactOutput = "Betas",
  regressionFamily = "binomial"
)

Arguments

depVarName	string name of class column (e.g., "class")
labelledDataFrame	data.frame with variable in columns and samples in rows; the last column should be labeled 'Class' and be 0 or 1 values.
stdBetas	logical to use standardized beta coefficients.
absBetas	logical to use absolute value of beta coefficients.
numCores	numeric number of processor cores to use in mclapply
verbose	logical to send verbose messages to stdout.
writeBetas	logical indicating whether to write beta values to separate file.
interactOutput	string output in return matrix, "indicating betas "Betas", "stdBetas", "Pvals".
regressionFamily	string glm regression family name.

Value

regainMatrix matrix of variable by variable regression coefficients.

References

• http://www.nature.com/gene/journal/v11/n8/full/gene201037a.html Genes & Immunity Paper

• https://github.com/hexhead/inbixC++ inbix on github

See Also

Other GAIN functions: dcgain(), dmgain(), fitInteractionModel(), fitMainEffectModel(), gainToSimpleSIF(), getInteractionEffects(), getMainEffects(), regain()

Other inbix synonym functions: dcgain(), getMainEffects(), regain()

Examples

data(testdata10)
rinbixRegain <- regainParallel(testdata10, stdBetas = TRUE, absBetas = TRUE)

insilico/npdro documentation built on July 1, 2023, 2:56 p.m.