Docs updated, README updated.

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: haploR
 Type: Package
-Title: Query Haploreg and RegulomeDB
+Title: Query HaploReg and RegulomeDB
 Version: 1.4.1
 Date: 2016-12-30
 Author: I. Y. Zhbannikov, K. G. Arbeev, A. I. Yashin
 Maintainer: Ilya Y. Zhbannikov <[email protected]>
 Description: A set of utilities for querying 
-             Haploreg <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php> 
+             HaploReg <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php> 
              and RegulomeDB <http://www.regulomedb.org> web-based tools. The package connects to 
              Haploreg or RegulomeDB, searches and downloads results, without 
              opening web pages, directly from R environment. 

R/haploreg.R

@@ -1,4 +1,4 @@
-#' This function queries Haploreg web-based tool and returns results.
+#' This function queries HaploReg web-based tool and returns results.
 #' 
 #' @param query Query (a vector of rsIDs).
 #' @param file A text file (one refSNP ID per line).
@@ -28,7 +28,7 @@
 #' Default: <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>
 #' @param verbose Verbosing output. Default: FALSE.
 #' @return A data frame (table) with results similar to 
-#' Haploreg uses.
+#' HaploReg uses.
 #' @examples
 #' data <- queryHaploreg(c("rs10048158","rs4791078"))
 #' head(data)
@@ -101,4 +101,4 @@ queryHaploreg <- function(query=NULL, file=NULL,
     }
 
     return(res.table)
-}
+}

R/haploregStudy.R

@@ -1,7 +1,7 @@
-#' This function queries Haploreg web-based tool 
+#' This function queries HaploReg web-based tool 
 #' in order to see a list of GWAS.
 #' 
-#' @param url A url to Haploreg.
+#' @param url A url to HaploReg.
 #' Default: <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>
 #' @return A list of studies. Each study is itself a list
 #' of two: \code{name}, \code{id}.
@@ -23,4 +23,4 @@ getStudyList <- function(url="http://archive.broadinstitute.org/mammals/haploreg
                     function(n) {study <- list(name=names[n], id=ids[[n]])})
 
   return(studies)
-}
+}

README.md

@@ -1,4 +1,4 @@
-# haploR: utilities for querying Haploreg and other similar web-based tools
+# haploR: utilities for querying HaploReg and other similar web-based tools
 
 ## Installation
 
@@ -8,12 +8,12 @@ The last version of `haploR` that is compatible with the current version of R (3
 which can be downloaded using devtools:
 
 ```
-devtools::install_github("izhbannikov/haploR")
+devtools::install_github("izhbannikov/haploR", buildVignette=TRUE)
 ```
 
 ## Usage
 
-### Querying Haploreg
+### Querying HaploReg
 
 ```
 library(haploR)

vignettes/haplor-vignette.Rmd

@@ -1,5 +1,5 @@
 ---
-title: 'Using haploR, an R package for querying Haploreg and RegulomeDB'
+title: 'Using haploR, an R package for querying HaploReg and RegulomeDB'
 author: "Ilya Y. Zhbannikov"
 date: "`r date()`"
 output: html_document
@@ -12,15 +12,15 @@ vignette: >
 
 ## Overview
 
-Haploreg <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php> and 
+HaploReg <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php> and 
 RegulomeDB <http://www.regulomedb.org>
 are web-based tools that extracts biological information such as eQTL, 
 LD, motifs, etc. from large genomic projects such as ENCODE, 
 the 1000 Genomes Project, Roadmap Epigenomics Project and others. 
 This is sometimes called "post-GWAS" analysis.
 
 The R-package \texttt{haploR} was developed to query 
-those tools (Haploreg and RegulomeDB) directly from 
+those tools (HaploReg and RegulomeDB) directly from 
 \texttt{R} in order to facilitate high-throughput 
 genomic data analysis. Below we provide several examples 
 that show how to work with this package.
@@ -43,7 +43,7 @@ devtools::install_github("izhbannikov/haplor", buildVignette=TRUE)
 
 ## Examples
 
-### Querying Haploreg
+### Querying HaploReg
 #### One or several genetic variants
 
 ```{r, echo=TRUE, message=FALSE}
@@ -53,7 +53,7 @@ head(results)
 ```
 
 Here \texttt{query} is a vector with names of genetic variants. 
-\texttt{results} are the table similar to the output of Haploreg.
+\texttt{results} are the table similar to the output of HaploReg.
 
 #### Uploading file with variants
 
@@ -72,7 +72,7 @@ head(results)
 Sometimes you would like to explore results from 
 already performed study. In this case you should 
 first the explore existing studies from 
-Haploreg web site and then use one of 
+HaploReg web site and then use one of 
 them as an input parameter. See example below:
 
 ```{r, echo=TRUE, message=FALSE}