OUTRIDER: OUTRIDER - Finding expression outlier events

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

OUTRIDER - Finding expression outlier events

Description

The OUTRIDER function runs the default OUTRIDER pipeline combinig the fit, the computation of Z scores and P-values. All computed values are returned as an OutriderDataSet object.

To have more control over each analysis step, one can call each function separately.

1. estimateSizeFactors to calculate the sizeFactors

2. controlForConfounders to control for confounding effects

3. fit to fit the negative binomial model (only needed if the autoencoder is not used)

4. computePvalues to calculate the nominal and adjusted P-values

5. computeZscores to calculate the Z scores

Usage

OUTRIDER(
  ods,
  q,
  controlData = TRUE,
  implementation = "autoencoder",
  subsets = NULL,
  BPPARAM = bpparam(),
  ...
)

Arguments

ods	An OutriderDataSet object
q	The encoding dimensions
controlData	If TRUE, the default, the raw counts are controled for confounders by the autoencoder
implementation	"autoencoder", the default, will use the autoencoder implementation. Also 'pca' and 'peer' can be used to control for confounding effects
subsets	A named list of named lists specifying any number of gene subsets (can differ per sample). For each subset, FDR correction will be limited to genes in the subset, and the FDR corrected pvalues stored as an assay in the ods object in addition to the transcriptome-wide FDR corrected pvalues. See the examples for how to use this argument.
BPPARAM	A BiocParallelParam instance to be used for parallel computing.
...	Further arguments passed on to controlForConfounders

Value

OutriderDataSet with all the computed values. The values are stored as assays and can be accessed by: assay(ods, 'value'). To get a full list of calculated values run: assayNames(ods)

Examples

ods <- makeExampleOutriderDataSet()
implementation <- 'autoencoder'

ods <- OUTRIDER(ods, implementation=implementation)

pValue(ods)[1:10,1:10]
res <- results(ods, all=TRUE)
res

plotAberrantPerSample(ods)
plotVolcano(ods, 1)

# example of restricting FDR correction to subsets of genes of interest 
genesOfInterest <- list("sample_1"=sample(rownames(ods), 3), 
                         "sample_2"=sample(rownames(ods), 8), 
                         "sample_6"=sample(rownames(ods), 5))
genesOfInterest
ods <- OUTRIDER(ods, subsets=list("exampleSubset"=genesOfInterest))
padj(ods, subsetName="exampleSubset")[1:10,1:10]
res <- results(ods, all=TRUE)
res

gagneurlab/OUTRIDER documentation built on April 29, 2024, 2:22 a.m.