Vignette

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: HTSanalyzeR2
 Type: Package
 Title: An R package for gene set enrichment and network analysis of various high-throughput data
-Version: 0.99.12
+Version: 0.99.13
 Author: Lina ZHU <zhulina0609@gmail.com>, Feng GAO <gaofeng21cn@gmail.com>, 
         Xiupei MEI <meixiupei@gmail.com>, Xin Wang <xinwang2hms@gmail.com>
 Maintainer: Lina ZHU <zhulina0609@gmail.com>

R/gsca_enrichmap.R

@@ -505,7 +505,8 @@ setMethod("viewEnrichMap", signature = "GSCA",
             options$label = list(text = gsNameType)
             options$colorScaler = "log10"
             options$nPermutations = object@para$nPermutations
-            defaultOptions = list(title = title, legendTitle = "-Log10(Adjusted p-values)", type = stringr::str_replace(resultName, ".results", ""))
+            defaultOptions = list(title = title, legendTitle = "-Log10(Adjusted p-values)",
+                                  type = stringr::str_replace(resultName, ".results", ""))
             graphOptions <- modifyList(defaultOptions, options)
 
             forceGraph(em_nodes, em_links, nMappings, lMappings, graphOptions, seriesData = series)

README.md

@@ -116,7 +116,7 @@ gsca2 <- analyze(gsca1,
                  para=list(pValueCutoff=0.05, pAdjustMethod="BH",
                            nPermutations=100, minGeneSetSize=180,
                            exponent=1), 
-                           doGSOA = TRUE)
+                           doGSOA = FALSE)
 
 ## append gene sets terms
 gsca3 <- appendGSTerms(gsca2, 
@@ -136,19 +136,3 @@ report(gsca3)
 ## Getting help
 
 Should you have any questions about this package, you can either email to the developers listed in the *DESCRIPTION* part of this package or create an issue in the [issue part](https://github.com/CityUHK-CompBio/HTSanalyzeR2/issues).
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inst/templates/app.R

@@ -86,7 +86,8 @@ create_data_table <- function(gscaObj, analysis, genesets) {
   res <- gscaObj@result[[analysis_to_show]][[genesets]]
   res <- trim_result(res, digits = 3)
 
-  gseaDispValue <- ifelse(is.null(gscaObj@para$nPermutations), "0", format((1/gscaObj@para$nPermutations), scientific=TRUE, digits = 1))
+  gseaDispValue <- ifelse(is.null(gscaObj@para$nPermutations), "0",
+                          paste("<", format((1/gscaObj@para$nPermutations), scientific=TRUE, digits = 1), sep = ""))
   jsRenders <- list(GSEA = colValueRender(gseaDispValue), HyperGeo = colValueRender('<1e-06'))
 
   columnDefs <- list(list(targets = which(colnames(res) == "HyperGeo.Adj.Pvalue") - 1, render = jsRenders[["HyperGeo"]]),

vignettes/bibliography.bib

@@ -86,4 +86,11 @@ @Article{Tzelepis2016
 }
 
 
-
+@Article{Sergushichev2016,
+author={Alexey Sergushichev},
+title={An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation},
+journal={bioRxiv},
+year={2016},
+url={http://biorxiv.org/content/early/2016/06/20/060012},
+doi = "10.1101/060012"
+}