Description Usage Arguments Value Author(s) See Also Examples
DEGreport::degCovariates()
wrapper supporting a bcbioRNASeq object.
1 2 3 4 5 | plotPCACovariates(object, ...)
## S4 method for signature 'bcbioRNASeq'
plotPCACovariates(object, metrics = TRUE,
normalized = c("rlog", "vst", "tmm", "tpm"), ...)
|
object |
Object. |
... |
Additional arguments, passed to |
metrics |
Include sample summary metrics as covariates. Defaults to
include all metrics columns ( |
normalized |
Character indicating which normalization method to apply:
|
ggplot
.
Lorena Pantano, Michael Steinbaugh
DEGreport::degCovariates()
.
DESeq2::rlog()
.
DESeq2::varianceStabilizingTransformation()
.
Other Quality Control Functions: plot5Prime3PrimeBias
,
plotCorrelationHeatmap
,
plotCountDensity
,
plotCountsPerGene
,
plotDispEsts
,
plotExonicMappingRate
,
plotGenderMarkers
,
plotGeneSaturation
,
plotGenesDetected
,
plotIntronicMappingRate
,
plotMappedReads
,
plotMappingRate
, plotMeanSD
,
plotPCA
, plotRRNAMappingRate
,
plotTotalReads
1 2 3 4 | plotPCACovariates(
object = bcb_small,
metrics = c("exonicRate", "intronicRate")
)
|
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