Updated the vignette

Author: Jain

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: TissueEnrich
 Type: Package
-Title: TissueEnrich
-Version: 0.99.12
-Authors@R: c(person("Ashish Jain", "Package Creator and Maintainer",
+Title: A tool to calculate tissue-specific gene enrichment
+Version: 0.99.13
+Authors@R: c(person("Ashish Jain",
         email="jain@iastate.edu",
-        role=c("aut", "cre")), person("Geetu Tuteja", "Package Maintainer",
+        role=c("aut", "cre")), person("Geetu Tuteja",
         email="geetu@iastate.edu",
         role=c("aut")))
 Description: The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.

README.md

@@ -2,7 +2,7 @@
 
 **Requirement**
 
-You need R version above 3.2 to run this application. Other dependencies are:
+You need R version above 3.5 to run this application. Other dependencies are:
 
 * `dplyr (>= 0.7.3)`
 * `ensurer (>= 1.1)`

vignettes/TissueEnrich.Rmd

@@ -101,8 +101,8 @@ The `output` is a list object containing the enrichment results. These results a
 
 ### Exploring tissue-specific gene enrichment results
 
-#### Tissue-specific gene enrichment histogram using `ggplot2`
-The first object in the `output` list is a `SummarizedExperiment` object containing the $-Log_{10}(P-Value)$, corresponding to the tissue-specific gene enrichment, along with the number of tissue-specific genes in the input gene set. This object can be used to visualize tissue-specific gene enrichment in the form of a histogram.
+#### Tissue-specific gene enrichment bar chart using `ggplot2`
+The first object in the `output` list is a `SummarizedExperiment` object containing the $-Log_{10}(P-Value)$, corresponding to the tissue-specific gene enrichment, along with the number of tissue-specific genes in the input gene set. This object can be used to visualize tissue-specific gene enrichment in the form of a bar chart.
 
 ```{r eval=TRUE}
 seEnrichmentOutput<-output[[1]]