Bug in 'gsea' function ('phenoTest' package)
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Entering edit mode
@damien-croteau-chonka-13392
Last seen 3.7 years ago
Boston, MA, USA

Bug Description

I've found a bug in the "gsea" function in the "phenoTest" Bioconductor package that I've been able to reproduce below:

library("phenoTest")
library("GSEABase")
library("devtools")

# setup test data as in package vignette
set.seed(777)

data(eset)

Tumor.size <- rnorm(ncol(eset), 50, 2)
pData(eset) <- cbind(pData(eset), Tumor.size)
pData(eset)[1:20, 'lymph.node.status'] <- 'positive'

survival <- matrix(c("Relapse", "Months2Relapse"),
                   ncol = 2,
                   byrow = TRUE)
colnames(survival) <- c('event', 'time')
vars2test <-
    list(survival = survival,
         categorical = 'lymph.node.status',
         continuous = 'Tumor.size')

epheno <- ExpressionPhenoTest(eset,vars2test,p.adjust.method='none')

sign1 <- sample(featureNames(eset))[1:20]
sign2 <- sample(featureNames(eset))[1:50]
mySignature <- list(sign1, sign2)
names(mySignature) <- c('My first signature', 'Another signature')

myGeneSetA <- GeneSet(geneIds = sign1, setName = 'My first signature')
myGeneSetB <- GeneSet(geneIds = sign2, setName = 'Another signature')
mySignature <- GeneSetCollection(myGeneSetA, myGeneSetB)

The example gene set enrichment analysis (GSEA) from the vignette runs fine:

my.gsea <-
    gsea(
        x = epheno,
        gsets = mySignature,
        B = 1000,
        p.adjust = 'BH',
        center = TRUE,
        pval.comp.method = "original"
    )

A customized GSEA does not run fine:

my.gsea2 <-
    gsea(
        x = epheno,
        gsets = mySignature,
        B = 1000,
        p.adjust = 'BH',
        pval.comp.method = "signed" # [KEY CHANGE]
    )

# Error in getNesPval(nes, pval.comp.method, pval.smooth.tail) : 
#     object 'escore' not found

I've commented the test code above to highlight the key parameter change that reveals the bug. If I follow the traceback, I land here:

traceback()

# 13: getNesPval(nes, pval.comp.method, pval.smooth.tail)
# 12: gseaSignificance(x, y, pval.comp.method, pval.smooth.tail)
# 11: (function (x, y, z) 
#     gseaSignificance(x, y, pval.comp.method, pval.smooth.tail))(x = dots[[1L]][[1L]], 
#         y = dots[[2L]][[1L]])
# 10: mapply(function(x, y, z) gseaSignificance(x, y, pval.comp.method, 
#         pval.smooth.tail), x = es, y = es.sim)
# 9: getSummary(es, es.sim, fchr, p.adjust.method = p.adjust.method, 
#        pval.comp.method, pval.smooth.tail, signatures, test, fewGsets)
# 8: cbind(n = unlist(lapply(x$s, length)), getSummary(es, es.sim, 
#        fchr, p.adjust.method = p.adjust.method, pval.comp.method, 
#        pval.smooth.tail, signatures, test, fewGsets))
# 7: gseaSignificance(x, p.adjust.method, pval.comp.method, pval.smooth.tail)
# 6: gseaSignificance(x, p.adjust.method, pval.comp.method, pval.smooth.tail)
# 5: FUN(X[[i]], ...)
# 4: lapply(x, function(x) gseaSignificance(x, p.adjust.method, pval.comp.method, 
#        pval.smooth.tail))
# 3: gseaSignificance(sim, p.adjust.method = p.adjust.method, pval.comp.method = pval.comp.method, 
#        pval.smooth.tail = pval.smooth.tail)
# 2: gseaSignificance(sim, p.adjust.method = p.adjust.method, pval.comp.method = pval.comp.method, 
#        pval.smooth.tail = pval.smooth.tail)
# 1: gsea(x = epheno, gsets = mySignature, B = 1000, p.adjust = "BH", 
#        pval.comp.method = "signed")

Possible Solution

Here is a link to the line in the current package source where the traceback stops (https://github.com/Bioconductor-mirror/phenoTest/blob/release-3.5/R/gsea.R#L286).

The internal "getNesPval" function itself is defined above (https://github.com/Bioconductor-mirror/phenoTest/blob/release-3.5/R/gsea.R#L194)

It appears that the "escore" variable needed deep inside the "getNesPval" function is not defined there (https://github.com/Bioconductor-mirror/phenoTest/blob/release-3.5/R/gsea.R#L213).

While in debug mode, if I manually redefined the "getNesPval" function to include "escore" as a parameter, the top-level "gsea" command was able to finish successfully.

Session Info

session_info()

# Session info -------------------------------------------------------------------------------------------
#  setting  value                       
#  version  R version 3.4.0 (2017-04-21)
#  system   x86_64, linux-gnu           
#  ui       RStudio (1.0.143)           
#  language (EN)                        
#  collate  en_US.UTF-8                 
#  tz       <NA>                        
#  date     2017-08-31                  
# 
# Packages -----------------------------------------------------------------------------------------------
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#  gmp                    0.5-13.1 2017-03-10 CRAN (R 3.4.0)
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phenoTest • 1.1k views
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