initialize.project: Intialize the Project Environment

In robustSingleCell: Robust Clustering of Single Cell RNA-Seq Data

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

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())

robustSingleCell documentation built on May 2, 2019, 2:11 p.m.