Description Usage Arguments Details Value Author(s) References Examples
This function ranks genes based on differential expression analytic method.
1 2 | geneRanker(expmat1, expmat2, genes,
rankers = c("ttest", "SAM", "Limma"), verbose = FALSE)
|
expmat1 |
a numeric matrix, gene expression matrix under condition 1. |
expmat2 |
a numeric matrix, gene expression matrix under condition 2. |
genes |
a character vector, genes to be analyzed. |
rankers |
a character vector, differential expression methods |
verbose |
logical. TRUE: intermediate results will be printed to the screen. |
Different methods can be selected. More information can be referred in GeneSelector package (Boulesteix and Slawski, 2009). To run this function, please first install geneSelector package with the commands: source("http://bioconductor.org/biocLite.R"); biocLite("GeneSelector")
A list containing different components:
ranker |
a numeric matrix containing gene rank, statistic and p-value from the ranker. |
dot |
a numeric matrix containing gene rank, statistic and p-value from the rankers. |
pvalMat |
a numeric matrix containing p-values from different rankers. |
Chuang Ma, Xiangfeng Wang.
[1] Boulesteix A-L and Slawski M. Stability and aggregation of ranked gene lists. Brief Bioinform, 2009, 10(5): 556-568.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
## Not run:
##differential expression analysis
res <- geneRanker(expmat1 = ControlExpMat, expmat2 = SaltExpMat,
genes = rownames(ControlExpMat)[1:100],
rankers = c("ttest", "SAM", "Limma"),
verbose = FALSE )
##the p-value for differential method
res$pvalMat[1:10,]
## End(Not run)
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