documentation cleanup

README.md

@@ -13,7 +13,7 @@ The `msigdbr` R package provides Molecular Signatures Database (MSigDB) gene set
 * as both gene symbols and Entrez Gene IDs (for better compatibility with pathway enrichment tools)
 * that can be used in a script without requiring additional external files
 
-Details and examples are described in the [vignette](https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html).
+Details and examples are described in the [vignette](https://CRAN.R-project.org/package=msigdbr/vignettes/msigdbr-intro.html).
 
 ## Installation
 

vignettes/msigdbr-intro.Rmd

@@ -4,7 +4,7 @@ output:
   rmarkdown::html_vignette:
     keep_md: true
 vignette: >
-  %\VignetteIndexEntry{Introduction to msigdbr}
+  %\VignetteIndexEntry{Introduction to the msigdbr package}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -14,7 +14,10 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
+# increase the screen width
 options(width = 90)
+# reduce the minimum number of characters for the tibble column titles
+options(pillar.min_title_chars = 8)
 ```
 
 ## Overview
@@ -76,6 +79,7 @@ The `msigdbr()` function output can also be manipulated as a standard data frame
 
 ```{r get-mouse-h-filter}
 m_df = msigdbr(species = "Mus musculus") %>% dplyr::filter(gs_cat == "H")
+head(m_df)
 ```
 
 ## Integrating with Pathway Analysis Packages
@@ -112,8 +116,8 @@ Which version of MSigDB was used?
 Can't I just download the gene sets from MSigDB?
 
 > Yes.
-> You can then import the GMTs with something like `getGmt()` from the `GSEABase` package.
-> Only human genes are available, even for gene sets generated with mouse data.
+> You can then import the GMT files with `getGmt()` from the `GSEABase` package.
+> The GMTs only include the human genes, even for gene sets generated from mouse data.
 > If you are not working with human data, you then have to convert the MSigDB genes to your organism or your genes to human.
 
 Can't I just convert between human and mouse genes by adjusting gene capitalization?