Set base project
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The following code will pop up a Rmd template and then clicking ‘save’ will populate that folder with HCBC data structure guidelines
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-rmarkdown::draft("project_folder",template="common",package="bcbioR")
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As well, You can get this by going to File -> New File -> R markdown: - then From Template, and choose bcbio base - choose the folder to deploy files, it could be a new folder or an existing one
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use setwd() to set your current directory to the place where you want to work. The bcbioR functions will automatically write to whatever directory you have set.
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setwd("/path/to/analysis/folder")
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The following code will pop up a Rmd template will populate that folder with HCBC data structure guidelines
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bcbio_templates(type="base", outpath="/path/to/analysis/folder")
Set RNAseq report folder
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This code will populate the folder with HCBC data structure guidelines and Rmd code:
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This code will populate the folder with HCBC data structure guidelines and Rmd code: You do not need to create a reports folder prior to running this code. This will create and populate the reports folder.
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bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")