overlap

README

Module name: organelle-overlap

Takes two lists of proteins and a txt file with similarity scores between proteins and outputs metrics on the similarity within and between the lists.

parameters	definition	default
compartmentFile	JSON file with lists of proteins to compare
outFile	output file name	organelle-overlap.txt
similarityFile	three-column tsv file (with header)

Example file formats

compartmentFile

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

similarityFile (tab-separated)

source  target  similarity
a   a   1
a   b   0.5
a   c   0.25
b   a   0.5
b   b   1
b   c   0.35
c   a   0.25
c   b   0.35
c   c   1

Output (example)

median  mean    min     max
ER lumen        0.541   0.448   0.087   0.699
ER membrane     0.429   0.380   0.035   0.706
between 0.069   0.116   0.013   0.655

Documentation

Overview

Package overlap calculates overlap metrics between two lists of proteins

Index

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

Functions

func Metrics

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

Metrics uses a txt file with similarity scores between proteins and calculates metrics between and within two lists of proteins