rankmetrics

package
v0.0.0-...-40008dc Latest Latest
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 Go to latest Published: Jun 11, 2022 License: MIT Imports: 15 Imported by: 0

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

Constants

This section is empty.

Variables

This section is empty.

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.

Types

This section is empty.

Source Files

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