findEncodingDim: Find the optimal encoding dimension

Description Usage Arguments Value Examples

View source: R/method-gridSearch.R

Description

Finds the optimal encoding dimension for a given data set by running a grid search based on the provided parameter set.

Usage

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findEncodingDim(
  ods,
  params = seq(2, min(100, ncol(ods) - 1, nrow(ods) - 1), 2),
  freq = 0.01,
  zScore = 3,
  sdlog = log(1.6),
  lnorm = TRUE,
  inj = "both",
  ...,
  BPPARAM = bpparam()
)

findInjectZscore(
  ods,
  freq = 0.01,
  zScoreParams = c(seq(1.5, 4, 0.5), "lnorm"),
  encDimParams = c(seq(3, 40, 3), seq(45, 70, 5), 100, 130, 160),
  inj = "both",
  ...,
  BPPARAM = bpparam()
)

Arguments

ods

An OutriderDataSet

params, encDimParams

Set of possible q values.

freq

Frequency of outlier, defaults to 1E-2

zScore, zScoreParams

Set of possible injection Z-score, defaults to 3.

sdlog

Standard deviation of the sitribution on the log scale.

lnorm

If TRUE, the default, Z-scores are drawn from a log normal distribution with a mean of log(zScore) in log-scale.

inj

Injection strategy, by default 'both'.

...

Further arguments passed on to the controlForConfounders function.

BPPARAM

BPPARAM object by default bpparam().

Value

The optimal encoding dimension

Examples

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ods <- makeExampleOutriderDataSet()
encDimSearchParams <- c(5, 8, 10, 12, 15)
zScoreParams <- c(2, 3, 5, 'lnorm')
implementation <- 'autoencoder'
register(MulticoreParam(4))

ods1 <- findEncodingDim(ods, params=encDimSearchParams, 
        implementation=implementation)
plotEncDimSearch(ods1)

ods2 <- findInjectZscore(ods, zScoreParams=zScoreParams,
        encDimParams=encDimSearchParams, implementation=implementation)
plotEncDimSearch(ods2)

gagneurlab/OUTRIDER documentation built on Oct. 24, 2020, 6:49 p.m.