Description Usage Arguments Value
View source: R/RNASeqUtilities.R
Apply GSEA to a voom normalized data set for a specific model and coefficients.
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voomDat |
Eset of voom normalised data which must include the design. This is the output of voom function in limma. |
geneIndices |
List of gene indices corresponding to gene sets. It is created by ids2indices function in limma. |
coefs |
Vector of coefficients to test. They must map to a coefficient in the design matrix in 'voomDat'. |
labels |
Vector of character strings that labels each coefficient being tested. This allows for more human readable labels than the lmFit coefficients. Labels must map one to one to 'coefs'. |
onlySigs |
Boolean: if TRUE return only genesets that pass the 'FDRCut' threshold (return -1 if no significant gene sets) else return all genesets. Default is FALSE. |
FDRCut |
FDR threshold to use to determine significance. Default is 0.2. |
List of camera results. Each element is the result for a single coefficient from 'coefs'
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