Description Usage Arguments Details Value Author(s) References Examples
View source: R/PolyfitFunctions.R
Function to level out a P-value spectrum generated by the Polyfit extension of DESeq by fitting a quadratic function to the right hand portion of the spectrum, produce 'corrected' p-values and q-values using an adapted version of the Storey-Tibsharini procedure
1 | levelPValues(oldPvals, plot = FALSE)
|
oldPvals |
an array of p-values produced by the Polyfit replacement of the DESeq function pfNbinomTest() or the Plyfit replacement of the edgeR function pfExactTest() |
plot |
TRUE to plot original and corrected pvalue spectra; FALSE not to plot |
levelPValues
should only be used with P-values generated by the Polyfit function pfNbinomTest
, and not with P-values generated by nbinomTest
.
List containing
pi0estimate |
an estimate of the proportion of genes not differentially expressed |
lambdaOptimal |
the point in the p-value spectrum past which a quadratic is fitted |
pValueCorr |
p-values calculated from the levelled spectrum |
qValueCorr |
q-values calculated from the levelled spectrum |
qValueCorrBH |
q-values calculated from pValueCorr using Benjamini-Hochberg |
Conrad Burden
Burden, C.J., Qureshi, S. and Wilson, S.R. (2014). Error estimates for the analysis of differential expression from RNA-seq count data, PeerJ PrePrints 2:e400v1.
1 2 3 4 5 6 7 8 | cds <- makeExampleCountDataSet()
cds <- estimateSizeFactors( cds )
cds <- estimateDispersions( cds )
nbTPolyfit <- pfNbinomTest( cds, "A", "B" )
lP <- levelPValues(nbTPolyfit$pval, plot=TRUE)
pvalTab <- cbind(origPval=nbTPolyfit$pval, correctedPval=lP$pValueCorr)
cat("\n Original and corrected P-values from DESeq \n")
head(pvalTab)
|
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