transmembrane

README

Module name: assessment-transmembrane

Get information about the transmembrane proteins residing between two NMF compartments.

parameters	definition	default
basisMatrix	NMF basis matrix
cytosolicBaits	baits that were used to label the cytosolic compartment (comma-separated list)
cytosolicCompartments	ranks defining cytosolic compartments (comma-separated list)
fdr	FDR	0.01
minRankValue	minimum NMF score for a primary rank to include a prey in the analysis	0.15
lumenalBaits	baits that were used to label the lumenal compartment (comma-separated list)
lumenalCompartments	ranks defining lumenal compartments (comma-separated list)
outFile	list of preys with transmembrane domains and associated information	transmembrane.txt
saint	SAINT file

Example file formats

basisMatrix

variable,1,2,3
AAAS,0.0,0.18373784550412228,0.0
AAK1,0.13963834317658874,0.0,0.0
AAR2,0.0,0.016517285371126216,0.034697999230769466
AARS2,0.0,0.0,0.001598769548285137

Output

• transmembrane.txt

Documentation

Overview

Package transmembrane reports the orientation evidence for transmembrane preys.

Index

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

Functions

func Orientation

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

Orientation takes all transmembrane proteins residing between a pair/set of organelles and reports evidence for cytosolic or lumenal orientation/regions.