README.md

In ehfhcrc/ImmSigPkg: Run HIPC ImmuneSignatures Pipeline from ImmuneSpace data

About ImmSigPkg

Last Updated: February 2017 Maintainer: Evan Henrich Contact: [e-mail]

A package of functions that allow the user to run the entire HIPC ImmuneSignatures Project Data Analysis Pipeline with original parameters from the published manuscript or with user-defined options.

Getting Started

To download and install the package for interactive work

library(devtools)
install_github("ehfhcrc/ImmSigPkg")
library(ImmSigPkg)

To see vignette:

# in console
git clone https://github.com/ehfhcrc/ImmSigPkg.git

# in R
setwd(<path_to_ImmSigPkg_source_code_dir>)
library(devtools)
build_vignettes()
# open vignette at <working_dir>/ImmSigPkg/Inst/Doc/Manuscript_Pipeline.html

Note: the vignette shows the output of the pipeline using the original parameters and takes approximately 45 minutes to build. At this time, it is recommended to build from source without compression by cloning the repo locally because there are unexplained differences between output for the old cohort when compressed versus built / knit directly. This may be due to an R environmental option used in the qusage() call within meta_analysis().

Running the Pipeline

To run the entire pipeline you can execute the function hipc_full_pipeline() and follow the prompts. It is recommended to use the original parameters for the first run to ensure things flow smoothly. This may take about 1 hour on your local machine. Once you have run everything through once and generated rawdata files (.txt) as well as .rds expressionSet files, you may run the meta analysis with different parameters using the command hipc_meta_analysis(). One point, this will write over your current result files.

Notes as of February 2017:

1. SDY80 rawdata is not yet able to be processed directly, pipeline uses original rawdata files provided by collaborators. Therefore, selecting "process SDY80 rawdata" when prompted will error out. This functionality will be incorporated as time permits.
2. SDY400 genetic expression data is not publicly available and the pipeline uses rawdata for baseline expression provided by the collaborators. This will be made public in Summer 2017 and will be incorporated as time permits.

ehfhcrc/ImmSigPkg documentation built on May 16, 2019, 12:16 a.m.