add trailing slashes to URLs

sistm · Feb 28, 2022 · 85e5a35 · 85e5a35
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diff --git a/R/TcGSA.LR.R b/R/TcGSA.LR.R
@@ -21,7 +21,7 @@
 #'@param gmt 
 #'a \bold{gmt} object containing the gene sets definition.  See
 #'\code{\link[GSA:GSA.read.gmt]{GSA.read.gmt}} and definition on 
-#'\href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats}{www.software.broadinstitute.org}.
+#'\href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats/}{www.software.broadinstitute.org}.
 #'
 #'@param design
 #'a matrix or dataframe containing the experimental variables that used in the model,

diff --git a/R/TcGSA.LR.parallel.R b/R/TcGSA.LR.parallel.R
@@ -35,7 +35,7 @@
 #'@param gmt 
 #'a \bold{gmt} object containing the gene sets definition.  See
 #'\code{\link[GSA:GSA.read.gmt]{GSA.read.gmt}} and definition on 
-#'\href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats}{www.software.broadinstitute.org}.
+#'\href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats/}{www.software.broadinstitute.org}.
 #'
 #'@param design
 #'a matrix or dataframe containing the experimental variables that used in the model,

diff --git a/R/plot1GS.R b/R/plot1GS.R
@@ -30,7 +30,7 @@
 #'@param gmt 
 #'a \bold{gmt} object containing the gene sets definition.  See
 #'\code{\link[GSA:GSA.read.gmt]{GSA.read.gmt}} and
-#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats}{www.software.broadinstitute.org}.
+#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats/}{www.software.broadinstitute.org}.
 #'
 #'@param Subject_ID 
 #'a factor of length \eqn{p} that is in the same order as the

diff --git a/R/plotMultipleGS.R b/R/plotMultipleGS.R
@@ -41,7 +41,7 @@
 #'@param gmt 
 #'a \bold{gmt} object containing the gene sets definition.  See
 #'\code{\link[GSA:GSA.read.gmt]{GSA.read.gmt}} and
-#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats}{www.software.broadinstitute.org}.
+#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats/}{www.software.broadinstitute.org}.
 #'
 #'@param Subject_ID 
 #'a factor of length \eqn{p} that is in the same order as the

diff --git a/R/plotPat.1GS.R b/R/plotPat.1GS.R
@@ -30,7 +30,7 @@
 #'@param gmt 
 #'a \bold{gmt} object containing the gene sets definition.  See
 #'\code{\link[GSA:GSA.read.gmt]{GSA.read.gmt}} and
-#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats}{www.software.broadinstitute.org}.
+#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats/}{www.software.broadinstitute.org}.
 #'
 #'@param Subject_ID 
 #'a factor of length \eqn{p} that is in the same order as the

diff --git a/R/plotSelect.GS.R b/R/plotSelect.GS.R
@@ -30,7 +30,7 @@
 #'@param gmt 
 #'a \bold{gmt} object containing the gene sets definition.  See
 #'\code{\link[GSA:GSA.read.gmt]{GSA.read.gmt}} and
-#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats}{www.software.broadinstitute.org}.
+#'definition on \href{https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats/}{www.software.broadinstitute.org}.
 #'
 #'@param Subject_ID 
 #'a factor of length \eqn{p} that is in the same order as the

diff --git a/README.Rmd b/README.Rmd
@@ -25,7 +25,7 @@ knitr::opts_chunk$set(
 
 On top of the CRAN help pdf-file, the following article explains what TcGSA is about:
 
->Hejblum, BP, Skinner, J, & Thiébaut, R (2015). Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. *PLOS Computational Biology*, **11**(6):e1004310. [<doi: 10.1371/journal.pcbi.1004310>](https://doi.org/10.1371/journal.pcbi.1004310)
+>Hejblum, BP, Skinner, J, & Thiébaut, R (2015). Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. *PLOS Computational Biology*, **11**(6):e1004310. [<doi: 10.1371/journal.pcbi.1004310>](https://doi.org/10.1371/journal.pcbi.1004310/)
 
 
 
@@ -47,7 +47,7 @@ The easiest way to get `TcGSA` is to install it from [CRAN](https://cran.r-proje
 install.packages("TcGSA")
 ```
 
-or to get the development version from [GitHub](https://github.com/sistm/TcGSA):
+or to get the development version from [GitHub](https://github.com/sistm/TcGSA/):
 ```{r GitHub-install, eval=FALSE}
 #install.packages("devtools")
 devtools::install_github("sistm/TcGSA")

diff --git a/man/TcGSA.LR.Rd b/man/TcGSA.LR.Rd
diff --git a/man/TcGSA.LR.parallel.Rd b/man/TcGSA.LR.parallel.Rd
diff --git a/man/plot1GS.Rd b/man/plot1GS.Rd
diff --git a/man/plotMultipleGS.Rd b/man/plotMultipleGS.Rd
diff --git a/man/plotPat.1GS.Rd b/man/plotPat.1GS.Rd
diff --git a/man/plotSelect.GS.Rd b/man/plotSelect.GS.Rd
diff --git a/vignettes/TcGSA_userguide.Rmd b/vignettes/TcGSA_userguide.Rmd
@@ -28,7 +28,7 @@ The `TcGSA` (Time-course Gene Set Analysis *Hejblum et al., 2015*) `R` package t
 gene expression dynamics for significance in gene sets. A gene set is a group of genes, 
 known *a priori* to share a common biological function or to be co-expressed. `TcGSA` relies 
 on linear mixed model to take into account the potential heterogeneity of expression 
-within a gene set. For more details, check the [published article in PLOS Computational Biology](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004310).
+within a gene set. For more details, check the [published article in PLOS Computational Biology](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004310/).
 
 
 
@@ -86,7 +86,7 @@ you can (re-)build the `gmt` object yourself following the method below.
 ### Self-built gmt
 
 To self-build your `gmt` object, you have to prepare a `.gmt` file. This file 
-format is the tab delimited file which can be created with [this helpful website](https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29) from the Broad Institute. In this file, one row represents one gene set with:
+format is the tab delimited file which can be created with [this helpful website](https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29/) from the Broad Institute. In this file, one row represents one gene set with:
 
 - Column 1: name of the gene set
 - Column 2: description of the gene set
@@ -129,7 +129,7 @@ This example comes from *Hejblum et al., 2015* and DALIA-1 HIV therapeutic vacci
 * 1^st^ phase from week 0 to week 24 (before treatment interruption): the patients were under anti-retroviral treatment and received trial vaccine on week 0, 4, 8 and 12.
 * 2nd phase from week 24 to week 48 (after treatment interruption): for the follow-up of patients, none of trial vaccine has been injected and anti-retroviral treatments have been interrupted (except for health problems).
 
-Blood samples have been collected at each of the different measurement time points, for each subject, to study the dynamic of gene expression over time. For more details, check the article from Hejblum et al. [here](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004310).
+Blood samples have been collected at each of the different measurement time points, for each subject, to study the dynamic of gene expression over time. For more details, check the article from Hejblum et al. [here](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004310/).
 
 The data are publicly available on [GEO website](https://www.ncbi.nlm.nih.gov/geo/) with GEO access number 'GSE46734'. We will be using the `GEOquery` package to get the data files from GEO website (see appendix for more details on `GEOquery`)