plotGenderMarkers: Plot Sexually Dimorphic Gender Markers

In WeiSong-bio/roryk-bcbioRNASeq: RNA-Seq Utilities

Description

Plot Sexually Dimorphic Gender Markers

Usage

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

# 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.