Description Usage Arguments Value Author(s) References Examples
Create a DIDS plot for the specified gene.
1 | didsPlot(eset, gene='Fgfr2')
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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 |
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sorted |
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main |
Title of the plot. |
ylim |
Y-limits of the plot. |
ylab |
Y-label of the plot. |
cols |
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colCode |
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minkw |
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selection |
Creates a DIDS plot of the expression values of the specified gene.
Julian de Ruiter wrote this wrapper function of the original DIDS code. DIDS itself was written by Jorma de Ronde.
Identifying subgroup markers in heterogeneous populations. (J de Ronde, et al. 2013.)
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