results | R Documentation |

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.

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

`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 |

`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. |

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`

.

```
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
```

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