estimateBestQ: 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 by either Optimal Hard Thresholding or injecting artificial splicing outlier ratios while maximizing the precision-recall curve.

Usage

estimateBestQ(
  ods = NULL,
  zScoresOHT = NULL,
  useOHT = TRUE,
  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 object
zScoresOHT	A z-score matrix
useOHT	If TRUE (default), Optimal Hard Thresholding is used to estimate the optimal encoding dimension.
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 OutriderDataSet object with the optimal encoding dimension saved in the metadata

Examples

ods <- makeExampleOutriderDataSet()

# run OHT (default)
estimateBestQ(ods)

# run hyperparameter optimization (grid-search)
encDimSearchParams <- c(5, 8, 10, 12, 15)
zScoreParams <- c(2, 3, 5, 'lnorm')
implementation <- 'autoencoder'
register(MulticoreParam(4))

ods1 <- estimateBestQ(ods, useOHT=FALSE, params=encDimSearchParams, 
        implementation=implementation)
plotEncDimSearch(ods1)

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

gagneurlab/OUTRIDER documentation built on June 13, 2025, 9:43 a.m.