thegranderlab/mir34a_asrna_project
A repo facilitating the reproduction of figures in the miR34a asRNA (lncTAM34a) project.
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The package is designed to facilitate the reproduction of results associated with the miR34a asRNA project (also known as the lncTAM34a project). Many of the results in this project were derived from analysis of data where the analysis has included filtering, transformation, and statistical analysis. Due to the fact that the results may be affected by the way that these steps are carried out, it is essential for these to be accuratley recorded in detail and available to facilitate the transparency of the project. In addition, to make each analysis reproduciable, the availability of the raw data is required. For these reasons, we have designed this package which includes all steps to generate each figure included in the project as well as all of the raw data.
To simply review the code associated with a figure, the easiest method is to just have a look at the vignette.html file located in the vignette folder. This can be opened in your web broswer and you can simply click on the code tabs associated with the figure you are interested in. This requires no installation of the package. To recreate figures in real time, please follow the instructions below.
install.packages('devtools')
.install_github('GranderLab/miR34a_asRNA_project')
.library(miR34AasRNAproject)
.plotFigure
. The command does three things:plotFigure
function only takes one argument which is a character vector of length one specifying which figure to recreate. For example, to recreate Figure 1a, in R we would type plotFigure('Figure 1a')
. Supplementary figures can be recreated with the following syntax plotFigure('Supplementary Figure 1a')
and supplementary documents with plotFigure('Supplementary Document 1')
.It is important to note that each time you call plotFigure
on an individual figure, the origional R version and R package versions are re-installed. This takes some time to accomplish (maybe 2-5 minutes). For those interested in replicating all the figures (instead of a select few) you may use plotFigure("All figures")
. This will reproduce all figures in one file and, thus avoids rebuilding R and R packages multiple times.
Finally, raw data used to generate figures can be accessed with getData("Figure 1a")
but will only work with figures that have associated data.
We are more than happy to help you with any questions you might have or hear your suggestions. Please submit these via the repositories issues section.
For more advanced examination of the code, a brief description of the package's structure follows and serves as a roadmap which, hopefully, will aid in navigation of the package contents:
plotFigure
function is called, it is this .Rmd file that is used to replicate the analysis for the specified figure. The analysis uses the corresponding data stored in the "data" folder.plotFigure
function and all functions required to replicate the R and R package versions used in the analysis (see more below).plotFigure
function first replicates the R and R package versions used to originally perform the analysis before rendering the corresponding .Rmd file and opening the resulting .html file in the users web browser. This is to guarantee that subsequent changes to R or R packages do not change the results of the analyses in the future. To do this the liftr package and docker are utilised. The R and R package version specifications are located in "inst/docker/liftr.yml". The docker file that is output from the lift
function in the liftr package is also at this location.docker pull thegranderlab/mir34a_asrna_project