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. |
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 |
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:
|
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
|
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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