Read me

This repository contains data and code necessary to reproduce analysis from the article: Burdukiewicz M, Sobczyk P, Rödiger S, Duda-Madej A, Mackiewicz P, Kotulska M. (2017) Amyloidogenic motifs revealed by n-gram analysis (Scientific Reports 7 (1), 12961).

The analysis conducted in this article resulted in a predictor of amyloidogenicity AmyloGram, available as a R package (https://cran.r-project.org/package=AmyloGram) and a web server (www.smorfland.uni.wroc.pl/shiny/AmyloGram/).

How to reproduce the main part of the analysis?

Source analysis.R. Be warned that computations are time consuming.

How to generate results and plots for publication?

Run analysis_publication.R. This step can be executed even without performing the full analysis, because the partial results are avaible in the repository.

Repository structure

benchmark

Raw data and results of the benchmark.

data

Processed data used in the study:

• amyloid and non-amyloid sequences derived from AmyLoad database on 09.01.2016.
• amyloid and non-amyloid benchmark data from pep424 dataset.
• tableA.csv normalized table A from supplemental materials of Wozniak2014.
• AA_index_mk2.csv amino acid properties chosen by MK.

data exploration

Scripts used in the exploratory phase of data analysis. Usually undocumented. All exploratory scripts that were found useful were later incorporated into the analysis and belog to the functions directory.

functions

All functions necessary to repeat the analysis. Functions are documented using roxygen standard.

varia

Additional source files as the logo of the AmyloGram package.

R session information

All scripts used in this study are compatible with following versions of R and necessary packages:

R version 3.4.1 (2017-06-30)

Platform: x86_64-pc-linux-gnu (64-bit)

attached base packages:

• grid
• stats
• graphics
• grDevices
• utils
• datasets
• methods
• base

other attached packages:

• bindrcpp(v.0.2)
• dplyr(v.0.7.1)
• reshape2(v.1.4.2)
• xtable(v.1.8-2)
• seqinr(v.3.3-6)
• biogram(v.1.5)
• slam(v.0.1-40)
• ggrepel(v.0.6.5)
• gtable(v.0.2.0)
• gridExtra(v.2.2.1)
• ggplot2(v.2.2.1)

loaded via a namespace (and not attached):

• Rcpp(v.0.12.11)
• bindr(v.0.1)
• magrittr(v.1.5)
• partitions(v.1.9-18)
• bit(v.1.1-12)
• munsell(v.0.4.3)
• colorspace(v.1.3-2)
• R6(v.2.2.2)
• rlang(v.0.1.1)
• stringr(v.1.2.0)
• plyr(v.1.8.4)
• tools(v.3.4.1)
• digest(v.0.6.12)
• assertthat(v.0.2.0)
• ade4(v.1.7-6)
• lazyeval(v.0.2.0)
• tibble(v.1.3.3)
• gmp(v.0.5-13.1)
• glue(v.1.1.1)
• entropy(v.1.2.1)
• stringi(v.1.1.5)
• pander(v.0.6.0)
• compiler(v.3.4.1)
• scales(v.0.4.1)
• combinat(v.0.0-8)
• polynom(v.1.3-9)
• pkgconfig(v.2.0.1)