bseqsc_config: Setup BSeq-SC External Dependencies

In shenorrLab/bseqsc: Deconvolution of Bulk Sequencing Experiments using Single Cell Data

Description

Configure bseqsc by setting up CIBERSORT source code.

Usage

bseqsc_config(file = NULL, error = FALSE)

Arguments

file	path to the CIBERSORT source R code.
error	logical that indicates if an error should be thrown if configuration failed.

Details

BSeq-sc uses CIBERSORT to estimate cell type proportions, based on reference expression profiles. Due to licensing requirements, source code for this algorithm needs to be downloaded separately from its website http://cibersort.stanford.edu. It is released under the Stanford Non-Commercial License. In order to use it with bseqsc you will need to:

1. Got to http://cibersort.stanford.edu

2. Register and log in

3. Download the latest R source code from the Downloadsection.

4. Configure bseqsc by pointing it to the downloaded file. This is done using the function bseqsc_config, which will copy the given R source file into the R-data/bseqsc sub-directory in the user's home directory for subsequent usage:

bseqsc_config('path/to/downloaded/source/CIBERSORT.R')

Value

the path where the file was copied, or NULL if bseqsc is not correctly configured.

shenorrLab/bseqsc documentation built on May 29, 2019, 9:23 p.m.