results: Accessor function for the 'results' object in an...

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

Accessor function for the 'results' object in an OutriderDataSet object.

Description

This function assembles a results table of significant outlier events based on the given filter criteria. The table contains various information accumulated over the analysis pipeline.

Usage

results(object, ...)

## S4 method for signature 'OutriderDataSet'
results(
  object,
  padjCutoff = 0.05,
  zScoreCutoff = 0,
  round = 2,
  all = FALSE,
  returnTranscriptomewideResults = TRUE,
  ...
)

Arguments

object	An OutriderDataSet object
...	Additional arguments, currently not used
padjCutoff	The significant threshold to be applied
zScoreCutoff	If provided additionally a z score threshold is applied
round	Can be TRUE, defaults to 2, or an integer used for rounding with round to make the output more user friendly
all	By default FALSE, only significant read counts are listed in the results. If TRUE all results are assembled resulting in a data.table of length samples x genes.
returnTranscriptomewideResults	If FDR corrected pvalues for subsets of genes of interest have been calculated, this parameter indicates whether additionally the transcriptome-wide results should be returned as well (default), or whether only results for those subsets should be retrieved.

Value

A data.table where each row is an outlier event and the columns contain additional information about this event. In details the table contains:

• sampleID / geneID: The gene or sample ID as provided by the user, e.g. rowData(ods) and colData(ods), respectively.

• pValue / padjust: The nominal P-value and the FDR corrected P-value (transcriptome-wide) indicating the outlier status.

• zScore / l2fc: The z score and log_2 fold change as computed by computeZscores.

• rawcounts: The observed read counts.

• normcounts: The expected count given the fitted autoencoder model for the given gene-sample combination.

• meanRawcounts / meanCorrected: For this gene, the mean of the observed or expected counts, respectively, given the fitted autoencoder model.

• theta: The dispersion parameter of the NB distribution for the given gene.

• aberrant: The transcriptome-wide outlier status of this event: TRUE or FALSE.

• AberrantBySample / AberrantByGene: Number of outliers for the given sample or gene (transcriptome-wide), respectively.

• padj_rank: Rank of this outlier event within the given sample.

• padjust_FDRset: The FDR corrected P-value with respect to the gene subset called 'FDRset', if gene subsets were specified during the P-value computation. Find more details at computePvalues.

Examples

ods <- makeExampleOutriderDataSet()

ods <- OUTRIDER(ods)

res <- results(ods, all=TRUE)
res

# example of retrieving results with FDR correction limited to a 
# set 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 <- computePvalues(ods, subsets=list("exampleSubset"=genesOfInterest))
res <- results(ods, all=TRUE, returnTranscriptomewideResults=FALSE)
res

gagneurlab/OUTRIDER documentation built on May 17, 2023, 3:51 p.m.