createProject: Create a new RNASeqPipeline project

Description Usage Arguments Details Examples

View source: R/RNASeqPipelineR.R

Description

Create the skeleton for a new RNASeqPipeline project.

Usage

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createProject(project_name, path = ".", verbose = FALSE,
  load_from_immport = FALSE)

Arguments

project_name

character name (ie, subdirectory) for project

path

character Root directory for project

verbose

logical Should verbose output be given?

load_from_immport

logical Creates a 'Tab' directory for Immport tables if the data are loaded from Immport.

Details

createProject will create a new RNASeqPipeline project under directory 'project_name' in the path specified by 'path'. The function creates the directory structure libraryd by RNASeqPipeline within the new project directory, including locations for fastQ files, fastQC output, RSEM quantification, and optionally GEO and SRA files if the data must be downloaded or linked to a GEO accession. Standard locations will also be provided to annotate the data utilizing the Immport schema. If the project exists, it will load the configuration if it can find it, otherwise it will proceed to re-configure the project.

Examples

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# construct a projects skeleton in a new folder titled "myproject".
createProject("myproject",path=".")
createProject("myproject",path=".",verbose=TRUE)
## Not run: 
createProject("myproject",path=".",load_from_immport=TRUE) #won't work unless immport is set up

## End(Not run)

RGLab/RNASeqPipelineR documentation built on Jan. 19, 2020, 12:31 a.m.