findEncodingDim: Find the optimal encoding dimension

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Find the optimal encoding dimension

Description

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

Usage

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

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 April 29, 2024, 2:22 a.m.