runCamera | R Documentation |
A funtion to perform gene enrichment analysis using rotational test (fry or camera) implemented in limma package.
runCamera(
exprMat,
design,
gmtFile,
id = NULL,
contrast = ncol(design),
method = "camera",
pCut = 0.05,
ifFDR = FALSE,
removePrefix = NULL,
plotTitle = "",
insideLegend = FALSE
)
exprMat |
Gene expression matrix. Genes as rows and samples as columns. |
design |
Design matrix as used by limma. |
gmtFile |
A path to the gene signature file. |
id |
A character vector of identifiers for genes used in the gmt file, ff the row names are not the same as the identfiers in the gmt file. |
contrast |
The index of the colum in design matrix that should be used as contrast for enrichment analysis. Default is the last column. |
method |
Wheter using "camera" (competitive) or "fry" (self-contained) method |
pCut |
Cut-off for significance of enrichment. |
removePrefix |
Remove a certain string in the set names to make them shorter. For example, "HALLMARK_". |
plotTitle |
The tilte used for enrichment bar plot. |
ifDFR |
Whether raw p value or adjusted p value (FDR) should be used for significance cut-off |
insideLegned |
Whether to put the legend inside the bar plot to save space. |
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