Merge branch 'master' into haldane

Fixing typo in vignette which referred to the older package name, manhattan
stephenturner · May 16, 2014 · 939c50d · 939c50d
2 parents aa9b635 + 8c856e9
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qqman
 Title: Q-Q and manhattan plots for GWAS data
-Version: 0.1.0
+Version: 0.1.1
 Author: Stephen Turner <[email protected]>
 Maintainer: Stephen Turner <[email protected]>
 Description: Q-Q and manhattan plots for GWAS data

diff --git a/inst/doc/qqman.Rmd b/inst/doc/qqman.Rmd
@@ -44,7 +44,7 @@ gwasResults <- d
 save(gwasResults, file="data/gwasResults.RData")
 ```
 
-The **manhattan** package includes functions for creating manhattan plots and q-q plots from GWAS results. The `gwasResults` data.frame included with the package has simulated results for 16,470 SNPs on 22 chromosomes. Take a look at the data:
+The **qqman** package includes functions for creating manhattan plots and q-q plots from GWAS results. The `gwasResults` data.frame included with the package has simulated results for 16,470 SNPs on 22 chromosomes. Take a look at the data:
 
 ```{r}
 str(gwasResults)

diff --git a/inst/doc/qqman.html b/inst/doc/qqman.html
@@ -60,35 +60,36 @@
 body {
   max-width: 800px;
   margin: auto;
+  padding: 1em;
   line-height: 20px;
 }
 
 tt, code, pre {
    font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace;
 }
 
-h1 { 
-   font-size:2.2em; 
+h1 {
+   font-size:2.2em;
 }
 
-h2 { 
-   font-size:1.8em; 
+h2 {
+   font-size:1.8em;
 }
 
-h3 { 
-   font-size:1.4em; 
+h3 {
+   font-size:1.4em;
 }
 
-h4 { 
-   font-size:1.0em; 
+h4 {
+   font-size:1.0em;
 }
 
-h5 { 
-   font-size:0.9em; 
+h5 {
+   font-size:0.9em;
 }
 
-h6 { 
-   font-size:0.8em; 
+h6 {
+   font-size:0.8em;
 }
 
 a:visited {
@@ -132,54 +133,54 @@
 }
 
 @media print {
-   * { 
-      background: transparent !important; 
-      color: black !important; 
-      filter:none !important; 
-      -ms-filter: none !important; 
+   * {
+      background: transparent !important;
+      color: black !important;
+      filter:none !important;
+      -ms-filter: none !important;
    }
 
-   body { 
-      font-size:12pt; 
-      max-width:100%; 
+   body {
+      font-size:12pt;
+      max-width:100%;
    }
-       
-   a, a:visited { 
-      text-decoration: underline; 
+
+   a, a:visited {
+      text-decoration: underline;
    }
 
-   hr { 
+   hr {
       visibility: hidden;
       page-break-before: always;
    }
 
-   pre, blockquote { 
-      padding-right: 1em; 
-      page-break-inside: avoid; 
+   pre, blockquote {
+      padding-right: 1em;
+      page-break-inside: avoid;
    }
 
-   tr, img { 
-      page-break-inside: avoid; 
+   tr, img {
+      page-break-inside: avoid;
    }
 
-   img { 
-      max-width: 100% !important; 
+   img {
+      max-width: 100% !important;
    }
 
-   @page :left { 
-      margin: 15mm 20mm 15mm 10mm; 
+   @page :left {
+      margin: 15mm 20mm 15mm 10mm;
    }
-     
-   @page :right { 
-      margin: 15mm 10mm 15mm 20mm; 
+
+   @page :right {
+      margin: 15mm 10mm 15mm 20mm;
    }
 
-   p, h2, h3 { 
-      orphans: 3; widows: 3; 
+   p, h2, h3 {
+      orphans: 3; widows: 3;
    }
 
-   h2, h3 { 
-      page-break-after: avoid; 
+   h2, h3 {
+      page-break-after: avoid;
    }
 }
 </style>
@@ -196,7 +197,7 @@
 
 <h1>Intro to the <strong>qqman</strong> package</h1>
 
-<p>The <strong>manhattan</strong> package includes functions for creating manhattan plots and q-q plots from GWAS results. The <code>gwasResults</code> data.frame included with the package has simulated results for 16,470 SNPs on 22 chromosomes. Take a look at the data:</p>
+<p>The <strong>qqman</strong> package includes functions for creating manhattan plots and q-q plots from GWAS results. The <code>gwasResults</code> data.frame included with the package has simulated results for 16,470 SNPs on 22 chromosomes. Take a look at the data:</p>
 
 <pre><code class="r">str(gwasResults)
 </code></pre>

diff --git a/vignettes/qqman.Rmd b/vignettes/qqman.Rmd
@@ -44,7 +44,7 @@ gwasResults <- d
 save(gwasResults, file="data/gwasResults.RData")
 ```
 
-The **manhattan** package includes functions for creating manhattan plots and q-q plots from GWAS results. The `gwasResults` data.frame included with the package has simulated results for 16,470 SNPs on 22 chromosomes. Take a look at the data:
+The **qqman** package includes functions for creating manhattan plots and q-q plots from GWAS results. The `gwasResults` data.frame included with the package has simulated results for 16,470 SNPs on 22 chromosomes. Take a look at the data:
 
 ```{r}
 str(gwasResults)