robustSingleCell (version 0.1.1)

initialize.project: Intialize the Project Environment

Description

Set up a project environment variable mapped to project results folder.

Usage

initialize.project(datasets, origins, experiments, data.path,
  work.path = NULL, marker.genes = NULL, clear.history = F,
  analysis.label = NULL, convert.to.mouse.gene.symbols = NULL)

Arguments

datasets

list of dataset code names

origins

list of dataset tissue origin/condition full name

experiments

list of experiment design annotations

data.path

path to where the data is located

work.path

path to where the analysis results are stored; optional, by default, a temporary directory

marker.genes

set of genes of interest for visualization purposes

clear.history

whether you would like to remove any previous project by this name

analysis.label

whether you would like to add a specific label to the analysis folder

convert.to.mouse.gene.symbols

whether you are using human gene symbols and would like to convert them to mouse gene symbols

Value

environment parameter containing file paths and experiment parameters

Examples

# NOT RUN {
data.path <- system.file("extdata", package = "robustSingleCell")
LCMV1_proj <- initialize.project(datasets = "LCMV1",
                            origins = "CD44+ cells",
                            experiments = "Rep1",
                            data.path = data.path,
                            work.path = tempdir())
# }