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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-05-01 14:58:43 UTC
  • mfrom: (1.1.4)
  • Revision ID: package-import@ubuntu.com-20130501145843-zfhxlxrouu8cx3tg
Tags: 1.7-4-1
* New upstream version 
* Updated qvalue package name (moved from CRAN to Bioconductor).
* Drop references to old name r-other-genabel.
* Drop build-dependance on package only suggested.
* Normalised VCS URLs following Lintian's standard.
* Acquire R:Depends directly from r-base-dev.
* Normalised control file with cme.

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R/grammar.R
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        if (method == "gamma") {
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                out <- qtscore(polyObject$pgresidualY,data=data,clambda=TRUE, ... )
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                # correct test and beta values
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                out@results[,"chi2.1df"] <- out[,"chi2.1df"]/polyObject$grammarGamma$Test
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                out@results[,"effB"] <- out[,"chi2.1df"]/polyObject$grammarGamma$Beta
 
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                out@results[,"chi2.1df"] <- out@results[,"chi2.1df"]/polyObject$grammarGamma$Test
 
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                out@results[,"effB"] <- out@results[,"effB"]/polyObject$grammarGamma$Beta
 
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                # re-compute standard errors (c2 = (b/se)^2; se = b/sqrt(c2))
 
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                out@results[,"se_effB"] <- abs(out@results[,"effB"])/sqrt(out@results[,"chi2.1df"])
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                # recompute p-values
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                out@results[,"P1df"] <- pchisq(out[,"chi2.1df"],df=1,lower.tail=FALSE)
 
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                out@results[,"P1df"] <- pchisq(out@results[,"chi2.1df"],df=1,lower.tail=FALSE)
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                # recompute Lambda
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                out@lambda <- estlambda(out[,"chi2.1df"],plot=FALSE,proportion=propPs)
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                if (out@lambda$estimate <= 1) {
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        # set uncorrectet stats to NA to avoid confusion
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        out@results[,"effAB"] <- out@results[,"effBB"] <- out@results[,"chi2.2df"] <- 
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                        out@results[,"P2df"] <- NA
 
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        out@call <- match.call()
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        # return results
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        return(out);
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}
 
 
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