shared

README

Module name: organelle-sharedregion

Takes two lists of proteins and outputs metrics on the regions (domains/motifs) shared between common preys.

parameters	definition	default
compartmentFile	JSON file with lists of proteins to compare
minPreyOccurrence	The minimum number of baits that a prey must be found with in each compartment	1
outFile	output file name	organelle-shared.txt
regionFile	text file with protein name and domains/motifs
saintFile	SAINT file

Example file formats

compartmentFile

[
  {
    "name": "compartment 1",
    "proteins": ["a", "b" ,"c"]
  },
  {
    "name": "compartment 2",
    "proteins": ["d", "e" ,"f"]
  }
]

regionFile (tab-separated, no header)

A1BG	disorder
A1BG	sig_p
A1CF	disorder
A1CF	low_complexity
A2M	disorder
A2M	low_complexity
A2M	sig_p
A2ML1	disorder
A2ML1	low_complexity
A2ML1	sig_p
A3GALT2	low_complexity
A3GALT2	transmembrane

Output (example)

region  no. preys  preys       preys not containing region
-       4          a, b, c, d
regionC 4          a, b, c, d
regionD 3          a, c, d     b
regionA 2          a, b        c, d
regionB 1          b           a, c, d

Documentation

Overview

Package shared outputs metrics on the regions found in preys shared by two lists of proteins

Index

• func Region(fileOptions map[string]interface{})

Functions

func Region

func Region(fileOptions map[string]interface{})

Region summarizes regions in preys shared between two lists of proteins