README.md

In NCI-CGR/cgrtelomeres: Automated Processing of Telomere qPCR Data

cgrtelomeres: automated variant of CGR qPCR telomere analysis

Overview

This is an R package designed to emulate the current series of tools and manual steps used by lab personnel to analyze their telomere qPCR data. This project was undertaken at the request of Casey Dagnall.

This project replicates the data output from the current analysis protocol (minus some Microsoft Office-specific things that aren't going to be in the final product). The data are packaged and processed via rmarkdown to make everything into a (reasonably) pretty and informative report.

Installation and Execution

R has the capacity to install packages directly from GitHub. In R:

# the following step is only required if you don't have the 'devtools' package installed yet

install.packages("devtools")

# the following steps are always required when launching R

require(devtools)

devtools::install_github("NCI-CGR/cgrtelomeres")

require(cgrtelomeres)

The primary entry point for the software is cgrtelomeres::process.experiment. You can get somewhat useful help documentation for this function in the usual R manner: ?cgrtelomeres::process.experiment. An example run command might be:

cgrtelomeres::process.experiment("/path/to/Examples for Bioinformatics", "/path/to/output_dir", "GP0317-TL7", "/path/to/PlateContentReport.xlsx", "/path/to/PlateList.xlsx")

I have not yet worked out how I want to deal with distribution of test data, so for the moment applicable parties can use the test dataset from the original email from Casey Dagnall. The input directory is not written to, so it's safe to use in place; just make sure "output_dir" doesn't point to anything important with existing workflow output.

Version History

• 04 February 2021: pre-alpha of v1.0.0

• 03 February 2021: migrated to NCI-CGR GitHub from GitLab.

• 09 October 2020: it minimally produces the output of Data/Analysis but it's not pretty. Plots and testing not implemented.

NCI-CGR/cgrtelomeres documentation built on Feb. 11, 2021, 12:12 p.m.