plotPCACovariates: Find Correlation Between Principal Components (PCs) and...

Description Usage Arguments Value Author(s) See Also Examples

Description

DEGreport::degCovariates() wrapper supporting a bcbioRNASeq object.

Usage

1
2
3
4
5
plotPCACovariates(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotPCACovariates(object, metrics = TRUE,
  normalized = c("rlog", "vst", "tmm", "tpm"), ...)

Arguments

object

Object.

...

Additional arguments, passed to DEGreport::degCovariates().

metrics

Include sample summary metrics as covariates. Defaults to include all metrics columns (TRUE), but desired columns can be specified here as a character vector.

normalized

Character indicating which normalization method to apply:

  • "tpm": Transcripts per million (tximport).

  • "tmm": edgeR trimmed mean of M-values. Calculated on the fly.

  • "rlog": DESeq2 log2 regularized log transformation.

  • "vst": DESeq2 log2 variance stabilizing transformation.

Value

ggplot.

Author(s)

Lorena Pantano, Michael Steinbaugh

See Also

Other Quality Control Functions: plot5Prime3PrimeBias, plotCorrelationHeatmap, plotCountDensity, plotCountsPerGene, plotDispEsts, plotExonicMappingRate, plotGenderMarkers, plotGeneSaturation, plotGenesDetected, plotIntronicMappingRate, plotMappedReads, plotMappingRate, plotMeanSD, plotPCA, plotRRNAMappingRate, plotTotalReads

Examples

1
2
3
4
plotPCACovariates(
    object = bcb_small,
    metrics = c("exonicRate", "intronicRate")
)

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.