fix typos in Manual and Tutorial

DESCRIPTION

@@ -5,7 +5,7 @@ Authors@R: c(person("Gregoire", "Versmee", email = "[email protected]",
 	     person("Laura", "Versmee", role = "aut"),
 	     person("Mikael", "Dusenne", role = "aut"),
 	     person("Niloofar", "Jalali", role = "aut"))
-Description: This package has been created to help users exploring, and downloading phenotic data from the database of Genotypes and Phenotypes (dbGaP)
+Description: This package has been created to help users exploring, downloading and decrypting phenotic and genomic data from the database of Genotypes and Phenotypes (dbGaP)
 URL: https://github.com/gversmee/dbgap2x
 BugReports: https://github.com/gversmee/dbgap2x/issues
 Depends:

Dockerfile

@@ -1,21 +1,21 @@
-FROM alpine/git as git
+FROM alpine/git:1.0.7 as git
 
 WORKDIR /root
 
 RUN git clone https://github.com/gversmee/dbgap2x.git
 
-FROM jupyter/base-notebook
+FROM jupyter/base-notebook:38f518466042
 
 LABEL maintainer="Gregoire Versmee <[email protected]>"
 
 RUN conda install --quiet --yes \
     'r-base=3.4.1' \
-    'r-irkernel=0.8*' \
-    'r-rcurl=1.95*' \
-    'r-xml' \
-    'r-data.table' \
-    'r-httr' \
-    'r-rlist' && \
+    'r-irkernel=0.8.*' \
+    'r-rcurl=1.95.*' \
+    'r-xml=3.98*' \
+    'r-data.table=1.12.*' \
+    'r-httr=1.*' \
+    'r-rlist=0.4.*' && \
     conda clean --all -f -y && \
     fix-permissions $CONDA_DIR
 
@@ -53,8 +53,9 @@ COPY --from=git /root/dbgap2x $HOME/dbgap2x
 RUN Rscript -e "install.packages('$HOME/dbgap2x', repos = NULL, type = 'source')" && \
 chown -R $NB_USER $HOME/dbgap2x && \
 chmod -R 4775 $HOME/dbgap2x && \
-jupyter trust $HOME/dbgap2x/dbgap2x.ipynb && \
 rm -rf $HOME/.local && \
 fix-permissions $HOME
 
+RUN jupyter trust $HOME/dbgap2x/dbgap2x.ipynb
+
 WORKDIR $HOME/dbgap2x

R/browse.dbgap.R

@@ -1,6 +1,6 @@
-#' @title Open the dbGap webpage of your study in your browser
+#' @title Open the dbGaP webpage of your study in your browser
 #'
-#' @param phs dbGap study ID (phs00xxxx, or 00xxxx, or xxx)
+#' @param phs dbGaP study ID (phs00xxxx, or 00xxxx, or xxx)
 #' @param no.browser set on TRUE will just display the URL
 #'
 #' @return Opens the dbGaP webpage of your study in your browser

R/browse.study.R

@@ -1,6 +1,6 @@
 #' @title Opens the study webpage in a web browser
 #'
-#' @param phs dbGap study ID (phs00xxxx, or 00xxxx, or xxx)
+#' @param phs dbGaP study ID (phs00xxxx, or 00xxxx, or xxx)
 #' @param no.browser set on TRUE will just display the URL
 #'
 #' @return Open the study webpage in a web browser

R/consent.groups.R

@@ -1,8 +1,8 @@
-#' @title Gets you the list of the consent groups of the study
+#' @title Gets the list of the study's consent groups
 #'
-#' @param phs dbGap study ID (phs00xxxx, or 00xxxx, or xxx)
+#' @param phs dbGaP study ID (phs00xxxx, or 00xxxx, or xxx)
 #'
-#' @return Returns a data frame with 3 cols : "consent group number", "cg short name" and "cg long name"
+#' @return Returns a data frame with 3 columns : "consent group number", "cg short name" and "cg long name"
 #'
 #' @author Gregoire Versmee, Laura Versmee, Mikael Dusenne, Niloofar Jalali
 

R/datatables.dict.R

@@ -1,8 +1,8 @@
-#' @title Create a tables dictionnary of your study
+#' @title Create study's tables dictionary
 #'
-#' @param phs dbGap study ID (phs00xxxx, or 00xxxx, or xxx)
+#' @param phs dbGaP study ID (phs00xxxx, or 00xxxx, or xxx)
 #'
-#' @return a data.frame with 3 cols : XXXXX
+#' @return a data.frame with 3 columns : table id (pht), table name (dt_study_name) and description (dt_label)
 #'
 #' @description This function extracts informations from data.dict.xml files from the dbgap ftp server to create a table dictionnary.
 #' @import XML

R/dbgap.data_dict.R

@@ -1,11 +1,11 @@
-#' @title Create a table dictionnary and a variable dictionnary
+#' @title Creates a table dictionary and a variable dictionary
 #'
 #' @param xml Folder where the xml files are located
 #' @param dest Folder where the data dictionnary and the table dictionnary will be extracted
 #'
 #' @return 2 csv files "phs_tables_dict.csv" and "phs_variables_dict.csv"
 #'
-#' @description This function extracts informations from data.dict xml files in dbgap to create table dictionnary and a variable dictionnary.
+#' @description This function extracts informations from data.dict xml files in dbgap to create table dictionary and a variable dictionary.
 #' @import XML
 #'
 #' @author Gregoire Versmee, Laura Versmee, Mikael Dusenne, Niloofar Jalali

R/dbgap.decrypt.R

@@ -1,9 +1,9 @@
-#' @title Decrypt ncbi_enc files
+#' @title Decrypts ncbi_enc files
 #'
-#' @return Decrypt the file(s) and replace it in the same folder
+#' @return Decrypts the file(s) and replaces it in the same folder
 #' @param file file or folder where your encrypted files are located
 #'
-#' @description This function decrypts dbGap files (*ncbi_enc) using your personnal key
+#' @description This function decrypts dbGaP files (*ncbi_enc) using your personal key
 #'
 #' @author Gregoire Versmee, Laura Versmee, Mikael Dusenne, Niloofar Jalali
 #' @export

R/is.parent.R

@@ -1,6 +1,6 @@
 #' @title Is the study a parent or a child study
 #'
-#' @param phs dbGap study ID (phs00xxxx, or 00xxxx, or xxx)
+#' @param phs dbGaP study ID (phs00xxxx, or 00xxxx, or xxx)
 #'
 #' @return Returns a logical TRUE if the study is a parent, and false if the study is a child
 #'

R/n.pop.R

@@ -1,11 +1,11 @@
-#' @title Gets the population number of the study
+#' @title Gets the study participants' number
 #'
-#' @param phs dbGap study ID (phs00xxxx, or 00xxxx, or xxx)
+#' @param phs dbGaP study ID (phs00xxxx, or 00xxxx, or xxx)
 #' @param consentgroup if false, will return only the total number of participants
 #'
-#' @return a data.frame with 2 cols : name of the consent group and n total. Possibility to add the breakdown by gender
+#' @return a data.frame with 2 columns : name of the consent group and n total. Possibility to add the breakdown by gender.
 #'
-#' @description This function extracts informations from data.dict.xml files from the dbgap ftp server to get the population characteristics. Works only for parents studies.
+#' @description This function extracts information from data.dict.xml files from the dbgap ftp server to get the population characteristics. Works only for parents studies.
 #' @import XML
 #' @import RCurl
 #'