release check 0.3.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: cRegulome
 Type: Package
-Version: 0.2.0
+Version: 0.3.0
 Title: Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
 Description: Builds a 'SQLite' database file of pre-calculated transcription 
     factor/microRNA-gene correlations (co-expression) in cancer from the 
@@ -10,7 +10,8 @@ Description: Builds a 'SQLite' database file of pre-calculated transcription
 License: GPL-3
 Authors@R: person("Mahmoud", "Ahmed",
     email = "mahmoud.s.fahmy@students.kasralainy.edu.eg",
-    role = c("aut", "cre"))
+    role = c("aut", "cre"),
+    comment = c(ORCID = "0000-0002-4377-6541"))
 URL: https://github.com/ropensci/cRegulome
 BugReports: https://github.com/ropensci/cRegulome/issues
 Encoding: UTF-8

NEWS.md

@@ -15,4 +15,13 @@
 # cRegulome 0.2.0
 
     - Reduced code dependencies
-    - Improved code performance
+    - Improved code performance
+
+# cRegulome 0.2.0
+
+    - Bug fix: since 0.2.0 the argument targets_only did not work  properly.
+    The bug is fixed and tested in this release.
+    - Added the option directed to cor_igraph which allowes for constructing
+    a directed graph when desired.
+    - Added the option to limit the query output of get_tf and get_mir to 
+    a predifined set of genes.

R/get_data.R

@@ -160,7 +160,7 @@ get_mir <- function(conn, mir, study, min_abs_cor, max_num,
         for(s in 1:length(study)) {
             # when targets are neither requested provided
             if(!targets_only & missing(targets)) {
-                # construct query statment
+                # construct query statement
                 stat <- stat_make(mir[m],
                                   study = study[s],
                                   min_abs_cor = min_abs_cor,
@@ -191,7 +191,7 @@ get_mir <- function(conn, mir, study, min_abs_cor, max_num,
                     tars <- intersect(tars, targets)
                 }
 
-                # construct a query statment, with targets
+                # construct a query statement, with targets
                 stat <- stat_make(mir[m],
                                   study = study[s],
                                   min_abs_cor = min_abs_cor,
@@ -324,7 +324,7 @@ get_tf <- function(conn, tf, study, min_abs_cor, max_num,
         for(s in 1:length(study)) {
             # when targets are neither requested provided
             if(!targets_only & missing(targets)) {
-                # construct query statment
+                # construct query statement
                 stat <- stat_make(tf[m],
                                   study = study[s],
                                   min_abs_cor = min_abs_cor,
@@ -359,7 +359,7 @@ get_tf <- function(conn, tf, study, min_abs_cor, max_num,
                     tars <- intersect(tars, targets)
                 }
 
-                # construct a query statment, with targets
+                # construct a query statement, with targets
                 stat <- stat_make(tf[m],
                                   study = study[s],
                                   min_abs_cor = min_abs_cor,
@@ -396,9 +396,9 @@ get_tf <- function(conn, tf, study, min_abs_cor, max_num,
     return(dat)
 }
 
-#' Make A SQL statment
+#' Make A SQL statement
 #' 
-#' Not meant to be called direclty by the user.
+#' Not meant to be called directly by the user.
 #'
 #' @param reg A \code{character} vector of one or more regulator ID.
 #' @param study A \code{character} vector of The Cancer Genome Atlas (TCGA)
@@ -497,7 +497,7 @@ stat_make <- function(reg, study, min_abs_cor, max_num, targets,
 
 #' Collect data from SQLite database
 #' 
-#' Not meant to be called direclty by the user.
+#' Not meant to be called directly by the user.
 #'
 #' @param conn A connection such as this returned by 
 #' \code{\link[DBI]{dbConnect}}
@@ -531,9 +531,9 @@ stat_collect <- function(conn, study, stat, type = 'mir') {
     return(df)
 }
 
-#' Make A SQL statment to extract target features
+#' Make A SQL statement to extract target features
 #' 
-#' Not meant to be called direclty by the user.
+#' Not meant to be called directly by the user.
 #'
 #' @inheritParams stat_make
 #' 
@@ -553,7 +553,7 @@ stat_make_targets <- function(reg, study, type = 'mir') {
 
 #' Collect target features from SQLite database
 #' 
-#' Not meant to be called direclty by the user.
+#' Not meant to be called directly by the user.
 #'
 #' @inheritParams stat_collect
 #'

R/methods.tidy.R

@@ -108,7 +108,7 @@ cor_tidy.cTF <- function(ob) {
 #' objects. 
 #' 
 #' @inheritParams cor_plot
-#' @param directed A \code{logical} when \code{FALSE} the graph is undirected
+#' @param directed A \code{logical} when \code{FALSE} the graph is indirected
 #'
 #' @return An \code{igraph} object 
 #' 
@@ -208,7 +208,7 @@ cor_igraph.cTF <- function(ob, directed = FALSE) {
 
 #' Prepare correlation data for plotting
 #' 
-#' Not meant to be called direclty by the user.
+#' Not meant to be called directly by the user.
 #'
 #' @param ob A \link{cmicroRNA} or \link{cTF} object such as this returned by
 #' calling \link{cmicroRNA} or \link{cTF}.
@@ -219,7 +219,7 @@ cor_igraph.cTF <- function(ob, directed = FALSE) {
 #' @param add_dir A \code{logical} default TRUE for whether to add a column
 #' called Direction that has the direction of the correlation; positive or 
 #' negative.
-#' @param add_corr A \code{logical} default TRUE for whether to add a colum
+#' @param add_corr A \code{logical} default TRUE for whether to add a column
 #' called Correlation that has the absolute value of the correlation
 #'
 #' @return A \code{data.frame}

README.md

@@ -2,7 +2,7 @@
 [![codecov](https://codecov.io/gh/ropensci/cRegulome/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/cRegulome)
 [![Build status](https://ci.appveyor.com/api/projects/status/gcmojtcsyt7rcwtk?svg=true)](https://ci.appveyor.com/project/ropensci/cregulome)
 [![](https://badges.ropensci.org/149_status.svg)](https://github.com/ropensci/onboarding/issues/149)  
-[![CRAN version](https://img.shields.io/badge/CRAN-v0.1.0-blue.svg)](https://CRAN.R-project.org/package=cRegulome) 
+[![CRAN version](https://img.shields.io/badge/CRAN-v0.3.0-blue.svg)](https://CRAN.R-project.org/package=cRegulome) 
 ![downloads](https://cranlogs.r-pkg.org/badges/grand-total/cRegulome)  
 
 # cRegulome  

cran-comments.md

@@ -35,3 +35,9 @@ This is a new release, so there are no reverse dependencies.
 * Submission v0.2.0
 * Reduced code dependencies
 * Improved code performance
+
+## v0.3.0
+
+* Submission v0.3.0
+* A bug fix
+* Minor changes to get_tf, get_mir and cor_igraph