general: General Arguments

Description Arguments Value

Description

General Arguments

Arguments

object

Object.

i

An integer or numeric scalar.

value

Value to assign.

x

Object.

...

Additional arguments.

alpha

Adjusted P value ("alpha") cutoff.

colData

data.frame describing the columns of the object. Must contain rownames identical to the colnames of the object.

color

Desired ggplot color scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual().

counts

Object containing a normalized counts matrix.

dir

Local directory path.

direction

Plot "both", "up", or "down" directions.

fill

Desired ggplot fill scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_fill_manual().

flip

Flip x and y axes.

gene2symbol

data.frame containing gene-to-symbol mappings. Must contain the columns geneID and geneName.

genes

Character vector of genes to include. These must match the rownames of the object. It is best practice to use the stable gene identifiers from Ensembl (e.g. "ENSG00000000003") and not the gene symbols.

headerLevel

R Markdown header level.

interestingGroups

Character vector denoting groups of interest that define the samples. If left unset, defaults to sampleName.

lfcThreshold

Log fold change ratio (base 2) cutoff threshold.

limit

Threshold to denote on the plot, using a dashed line.

minCounts

Minimum number of counts per gene in the counts matrix.

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.

ntop

Number of top genes to label.

passLimit

Threshold to plot pass color marker.

pointColor

Default point color for the plot.

results

DESeqResults object.

return

Object class to return. Uses match.arg() internally and picks the first item in the vector by default.

samples

Character vector of samples to include.

sigPointColor

character vector containing color names for labeling upregulated and downregulated genes. Also supports a character string for labeling DEGs with the same color, regardless of direction.

subtitle

Subtitle of plot.

title

Title of plot.

warnLimit

Threshold to plot warning color marker.

withDimnames

A logical, indicating whether dimnames should be applied to extracted assay elements.

Value

No value.


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