makeGeneTable {PathwaySplice} | R Documentation |
This function obtains genewise p-values, by representing each gene with the smallest p-value among its features, and then determines genes status as significant or not.
makeGeneTable(feature.table, sig.threshold = 0.05, stat = "pvalue")
feature.table |
An |
sig.threshold |
Significance threshold used to determine whether the gene is significant or not |
stat |
The statistic used to select significant genes. Options are 'pvalue' or 'fdr' |
Returns a genewised table with several variables (columns)
geneID |
Gene identifiers in ensembl gene IDs |
geneWisePvalue |
each gene is represented by the smallest p-value among its features |
numFeature |
number of gene features within the gene |
fdr |
false discovery rate for genewisePvalue |
sig.gene |
a gene is significant (1) or not (0) |
data(featureBasedData) gene.based.table <- makeGeneTable(featureBasedData)