Analysis of anchor screens
This script calculates residuals for anchor arms compared to the control arm
Author: Mudra Hegde
Email: mhegde@broadinstitute.org
Version: 1.0
Required packages
- pandas <= 0.16.2
- statsmodels
The code to run the hypergeometric analysis and the relevant chip file should be in the current working directory.
Inputs
- Input File: File with sgRNAs in first column, LFCs of control arm and anchor arms in following columns
- Chip File: File mapping sgRNAs to gene symbols; Default chip file: Brunello, CP0041
- Control: Column name of control arm
- Outputfolder: Folder to store all output files
To run this script, type the following on the terminal:
python anchor_analysis_v1.0 --input-file <Path to inputfile> --chip-file <Path to chip file> --control <Control column name> --outputfolder <Path to outputfolder>
Output file is a .txt file in the user-specified output folder with average residuals and average p-values per gene per anchor arm