# README

Module name: `control-preys`

Output statistics on prey proteins in controls using SAINT input files.

parameters	definition	default
bait	bait.dat file
enrichmentLimit	number of preys to user for GO enrichment after sorting	200
inter	bait.dat file
outFile	output file	control-preys.txt
outFileEnrichment	output file for GO enrichment	enrichment.txt
prey	bait.dat file

Example file formats

bait

bait.dat file from SAINT input. Add an extra (fourth) column specifying the type of control: empty, bira-flag, bira-gfp, etc. This file should be trimmed to remove any non-control samples.

128_7909	7909_BirAFLAG_April2017	C	bira-flag
128_9522	9522_BirAFLAG_April2017	C	bira-flag
128_8301	8301_FLAG_alone	C	empty
128_8310	8310_FLAG_alone	C	empty

inter

inter.dat file file from SAINT input.

128_7909	7909_BirAFLAG_April2017	BirA_R118G_H0QFJ5	1075	25
128_7909	7909_BirAFLAG_April2017	NP_000029.2	5	4
128_7909	7909_BirAFLAG_April2017	NP_000048.1	4	4
128_7909	7909_BirAFLAG_April2017	NP_000108.1	7	6

prey

prey.dat file file from SAINT input.

BirA_R118G_H0QFJ5	321	BirA_R118G_H0QFJ5
NP_000009.1	655	ACADVL
NP_000010.1	427	ACAT1
NP_000091.1	98	CSTB
NP_000099.2	509	DLD
NP_000131.2	423	FECH
NP_000150.1	438	GCDH
NP_000173.2	763	HADHA
NP_000217.2	623	KRT9
NP_000242.1	934	MSH2

Output

control-preys: list of preys found in controls and a breakdown of their abundance between the different types of controls

# Functions

Assess

Assess prey metrics for each prey interaction rank, such as the turnover rate, cellular abundance and number of lysines.