createNoisyDataset {GROAN}

Noisy Data Set Constructor

Description

This function creates a GROAN.NoisyDataset object (or fails trying). The class will contain all noisy data set components: genotypes and/or covariance matrix, phenotypes, strata (optional), a noise injector function and its parameters.
You can have a general description of the created object using the overridden print.GROAN.NoisyDataset function.

Usage

createNoisyDataset(
  name,
  genotypes = NULL,
  covariance = NULL,
  phenotypes,
  strata = NULL,
  extraCovariates = NULL,
  ploidy = 2,
  allowFractionalGenotypes = FALSE,
  noiseInjector = noiseInjector.dummy,
  ...
)

Arguments

name

A string defining the dataset name, used later do identify this particular instance in reports and result files. It is advisable for it to be it somewhat meaningful (to you, GROAN simply reports it as it is)

genotypes

Matrix or dataframe containing SNP genotypes, one row per sample (N), one column per marker (M), 0/1/2 format (for diploids) or 0/1/2.../ploidy in case of polyploids

covariance

matrix of covariances between samples of this dataset. It is usually a square (NxN) matrix, but rectangular matrices (NxW) are accepted to incapsulate covariances between samples in this set and samples of other sets. Please note that some regression models expect the covariance to be square and will fail on rectangular ones

phenotypes

numeric array, N slots

strata

array of M slots, describing the strata each data point belongs to. This is used for stratified crossvalidation (see createWorkbench)

extraCovariates

dataframe of optional extra covariates (N lines, one column per extra covariate). Numeric ones will be normalized, string and categorical ones will be transformed in stub TRUE/FALSE variables (one per possible value, see model.matrix).

ploidy

number of haploid sets in the cell. Defaults to 2 (diploid).

allowFractionalGenotypes

if TRUE non-integer values for genotypes can be allowed. Defaults to FALSE

noiseInjector

name of a noise injector function, defaults to noiseInjector.dummy

...

further arguments are passed along to noiseInjector

Value

a GROAN.NoisyDataset object.

See Also

GROAN.run createWorkbench

Examples

#For more complete examples see the package vignette
#creating a noisy dataset with normal noise
nds = createNoisyDataset(
  name = 'PEA, normal noise',
  genotypes = GROAN.KI$SNPs,
  phenotypes = GROAN.KI$yield,
  noiseInjector = noiseInjector.norm,
  mean = 0,
  sd = sd(GROAN.KI$yield) * 0.5
)