rankmetrics

README

Module name: interaction-rankmetrics

Calculates metrics for preys by interaction rank, including expression level, number of lysines and turnover rate.

parameters	definition	default
fdr	FDR threshold	0.01
fasta	sequence database in fasta format
gixDB	GIX database for parsing protein expression
turnoverFile	file with turnover rates per gene
outFile	output file	turnover-by-rank.txt
saint	SAINT file

Example file formats

fasta

>NP_001263222.1|gn|NISCH:11188| nischarin isoform 2 [Homo sapiens]
MATARTFGPEREAEPAKEARVVGSELVDTYTVYIIQVTDGSHEWTVKHRYSDFHDLHEKLVAERKIDKNL
LPPKKIIGKNSRSLVEKREKDLEVYLQKLLAAFPGVTPRVLAHFLHFHFYEINGITAALAEELFEKGEQL
LGAGEVFAIGPLQLYAVTEQLQQGKPTCASGDAKTDLGHILDFTCRLKYLKVSGTEGPFGTSNIQEQLLP
FDLSIFKSLHQVEISHCDAKHIRGLVASKPTLATLSVRFSATSMKEVLVPEASEFDEWEPEGTTLEGPVT
AVIPTWQALTTLDLSHNSISEIDESVKLIPKIEFLDLSHNGLLVVDNLQHLYNLVHLDLSYNKLSSLEGL
HTKLGNIKTLNLAGNLLESLSGLHKLYSLVNLDLRDNRIEQMEEVRSIGSLPCLEHVSLLNNPLSIIPDY
RTKVLAQFGERASEVCLDDTVTTEKELDTVEVLKAIQKAKEVKSKLSNPEKKGGEDSRLSAAPCIRPSSS
PPTVAPASASLPQPILSNQGNRVCILLLVEPHSPAWAPWLGWGWGRGASTCFQQGQTQGGQCLLQAGPRG
GTHGRGAWPDASCCLLGEDSQLL
>NP_001263218.1|gn|PRKAR1A:5573| cAMP-dependent protein kinase type I-alpha regulatory subunit isoform a [Homo sapiens]
MESGSTAASEEARSLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFERLEKEEAKQIQNLQK
AGTRTDSREDEISPPPPNPVVKGRRRRGAISAEVYTEEDAASYVRKVIPKDYKTMAALAKAIEKNVLFSH
LDDNERSDIFDAMFSVSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVGEGGSFGELALIYGTP
RAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQ
KIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKL
DRPRFERVLGPCSDILKRNIQQYNSFVSLSV

turnoverFile

PMID: 29414762, Supplementary table S3

Output

• turnover-by-rank.txt: table with turnover rate (mean and SD) and the number of genes with a turnover rate at each rank

prey rank turnover rate (mean) turnover rate (SD)  genes with turnover data

Documentation

Overview

Package rankmetrics calculates prey metrics for each prey interaction rank.

Index

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

Functions

func Calculate

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

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