plotGenderMarkers: Plot Sexually Dimorphic Gender Markers

Description Usage Arguments Value Author(s) See Also Examples

Description

Plot Sexually Dimorphic Gender Markers

Usage

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plotGenderMarkers(object, ...)

## S4 method for signature 'SummarizedExperiment'
plotGenderMarkers(object, ...)

## S4 method for signature 'bcbioRNASeq'
plotGenderMarkers(object, normalized = c("rlog",
  "vst", "tpm"), ...)

## S4 method for signature 'DESeqDataSet'
plotGenderMarkers(object, ...)

## S4 method for signature 'DESeqTransform'
plotGenderMarkers(object, ...)

Arguments

object

Object.

...

Additional arguments.

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)

Michael Steinbaugh

See Also

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

Examples

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# bcbioRNASeq ====
plotGenderMarkers(bcb_small)

# DESeqDataSet ====
plotGenderMarkers(dds_small)

# DESeqTransform ====
plotGenderMarkers(rld_small)

WeiSong-bio/roryk-bcbioRNASeq documentation built on July 6, 2019, 12:02 a.m.