From 85e5a353062fbc8250e68399dfe6a6e51da59fbe Mon Sep 17 00:00:00 2001 From: borishejblum Date: Mon, 28 Feb 2022 10:35:21 +0100 Subject: [PATCH] add trailing slashes to URLs --- R/TcGSA.LR.R | 2 +- R/TcGSA.LR.parallel.R | 2 +- R/plot1GS.R | 2 +- R/plotMultipleGS.R | 2 +- R/plotPat.1GS.R | 2 +- R/plotSelect.GS.R | 2 +- README.Rmd | 4 ++-- man/TcGSA.LR.Rd | 2 +- man/TcGSA.LR.parallel.Rd | 2 +- man/plot1GS.Rd | 2 +- man/plotMultipleGS.Rd | 2 +- man/plotPat.1GS.Rd | 2 +- man/plotSelect.GS.Rd | 2 +- vignettes/TcGSA_userguide.Rmd | 6 +++--- 14 files changed, 17 insertions(+), 17 deletions(-) diff --git a/R/TcGSA.LR.R b/R/TcGSA.LR.R index 5f620a8..dfd6148 100644 --- 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 index 5eeae95..e03f06f 100644 --- 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 index e0a7ef8..e5ce485 100644 --- 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 index 4cd4092..9eb6734 100644 --- 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 index 3f757db..a06ba61 100644 --- 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 index bf37cb6..6695eac 100644 --- 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 index 0ff19ff..1fd884f 100644 --- 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. [](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. [](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 index 3a9c05c..04c2bed 100644 --- a/man/TcGSA.LR.Rd +++ b/man/TcGSA.LR.Rd @@ -31,7 +31,7 @@ row.} \item{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}.} \item{design}{a matrix or dataframe containing the experimental variables that used in the model, namely \code{subject_name}, \code{time_name}, and \code{covariates_fixed} diff --git a/man/TcGSA.LR.parallel.Rd b/man/TcGSA.LR.parallel.Rd index 233b592..476a030 100644 --- a/man/TcGSA.LR.parallel.Rd +++ b/man/TcGSA.LR.parallel.Rd @@ -36,7 +36,7 @@ row.} \item{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}.} \item{design}{a matrix or dataframe containing the experimental variables that used in the model, namely \code{subject_name}, \code{time_name}, and \code{covariates_fixed} diff --git a/man/plot1GS.Rd b/man/plot1GS.Rd index 2878f34..4d23379 100644 --- a/man/plot1GS.Rd +++ b/man/plot1GS.Rd @@ -59,7 +59,7 @@ estimated gene expression, such as for the list returned in the \item{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}.} \item{Subject_ID}{a factor of length \eqn{p} that is in the same order as the columns of \code{expr} (when it is a dataframe) and that contains the patient diff --git a/man/plotMultipleGS.Rd b/man/plotMultipleGS.Rd index 3d857b4..9b60117 100644 --- a/man/plotMultipleGS.Rd +++ b/man/plotMultipleGS.Rd @@ -70,7 +70,7 @@ estimated gene expression, such as for the list returned in the \item{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}.} \item{Subject_ID}{a factor of length \eqn{p} that is in the same order as the columns of \code{expr} (when it is a dataframe) and that contains the patient diff --git a/man/plotPat.1GS.Rd b/man/plotPat.1GS.Rd index b3cd823..8330a67 100644 --- a/man/plotPat.1GS.Rd +++ b/man/plotPat.1GS.Rd @@ -52,7 +52,7 @@ estimated gene expression, such as for the list returned in the \item{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}.} \item{Subject_ID}{a factor of length \eqn{p} that is in the same order as the columns of \code{expr} (when it is a dataframe) and that contains the patient diff --git a/man/plotSelect.GS.Rd b/man/plotSelect.GS.Rd index 9ed59b8..a11a068 100644 --- a/man/plotSelect.GS.Rd +++ b/man/plotSelect.GS.Rd @@ -54,7 +54,7 @@ estimated gene expression, such as for the list returned in the \item{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}.} \item{Subject_ID}{a factor of length \eqn{p} that is in the same order as the columns of \code{expr} (when it is a dataframe) and that contains the patient diff --git a/vignettes/TcGSA_userguide.Rmd b/vignettes/TcGSA_userguide.Rmd index e1a42f3..f713c5e 100644 --- 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`)