didsPlot: Detection of Imbalanced Differential Signal (DIDS) - Plot

Description Usage Arguments Value Author(s) References Examples

View source: R/dids_wrapper.R

Description

Create a DIDS plot for the specified gene.

Usage

1
didsPlot(eset, gene='Fgfr2')

Arguments

eset

ExpressionSet object for which the plot should be made. The featureData of the object should either contain a column ‘symbol’ or another specified column (identified) by the geneSymbolCol parameter) that contains the gene symbol of each gene. The phenoData of the object should contain a ‘condition’ column that marks each sample as being either ‘sensitive’ or ‘resistant’. Note that this column may be ommitted if alternative grouping is provided by the groups parameter.

gene

Specifies which gene should be plotted (given as a gene symbol).

geneSymbolCol

Specifies an alternative column in which gene symbol information can be found.

groups

Specifies an alternative grouping of samples into two groups (overrides the condition column if present). Should be provided as a logical vector.

groupNames

Specifies the names of the two groups. Defaults to ‘sensitive’ and ‘resistant’.

densPlot

Specifies if the density plot should be created.

binclass
sorted
main

Title of the plot.

ylim

Y-limits of the plot.

ylab

Y-label of the plot.

cols
colCode
minkw
selection

Value

Creates a DIDS plot of the expression values of the specified gene.

Author(s)

Julian de Ruiter wrote this wrapper function of the original DIDS code. DIDS itself was written by Jorma de Ronde.

References

Identifying subgroup markers in heterogeneous populations. (J de Ronde, et al. 2013.)

Examples

1
2
res <- didsScore(eset)
didsPlot(eset, gene='Fgfr2')

NKI-CCB/dids documentation built on May 7, 2019, 6:02 p.m.