diff --git a/README.md b/README.md index 1db666d..1b8589b 100755 --- a/README.md +++ b/README.md @@ -28,6 +28,15 @@ library(devtools) install_github("ctlab/phantasusLite") ``` +Note that the latest version depends on `rhdfclient5 >= 1.25.1` from +Bioconductor 3.19, which on older systems can be more convenient to +install from GitHub: + +``` r +library(devtools) +install_github("vjcitn/rhdf5client") +``` + ## Dependencies To run the code you need: @@ -64,14 +73,13 @@ head(exprs(es)) ## GSM1281306 GSM1281307 Function loadCountsFromHSDS returns an ExpressionSet with the expression -matrix – the second exprs(es) contains an expression matrix. - -The remote repository URL is +matrix – now `exprs(es)` contains an expression matrix. The default +remote repository URL is ‘’. ``` r -url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' -es <- loadCountsFromHSDS(es, url) +# `url` is explicitly specified for illustration purposes and can be omitted +es <- loadCountsFromHSDS(es, url = 'https://alserglab.wustl.edu/hsds/?domain=/counts') head(exprs(es)) ``` diff --git a/README.rmd b/README.rmd index c13773c..85fdec5 100755 --- a/README.rmd +++ b/README.rmd @@ -28,6 +28,13 @@ library(devtools) install_github("ctlab/phantasusLite") ``` +Note that the latest version depends on `rhdfclient5 >= 1.25.1` from Bioconductor 3.19, which on older systems can be more convenient to install from GitHub: + +```{r message=FALSE, eval=FALSE} +library(devtools) +install_github("vjcitn/rhdf5client") +``` + ## Dependencies To run the code you need: @@ -61,13 +68,11 @@ ExpressionSet from the GEO doesn't contain the expression matrix -- `exprs(es)` head(exprs(es)) ``` -Function loadCountsFromHSDS returns an ExpressionSet with the expression matrix -- the second exprs(es) contains an expression matrix. - -The remote repository URL is ''. +Function loadCountsFromHSDS returns an ExpressionSet with the expression matrix -- now `exprs(es)` contains an expression matrix. The default remote repository URL is ''. ```{r} -url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' -es <- loadCountsFromHSDS(es, url) +# `url` is explicitly specified for illustration purposes and can be omitted +es <- loadCountsFromHSDS(es, url = 'https://alserglab.wustl.edu/hsds/?domain=/counts') head(exprs(es)) ```