Code for generating sequence coverage plots from NucleicAcidSearchEngine results
NucleicAcidSearchEngine (NASE) is a sequence database search engine for tandem mass spectrometry data of RNA oligonucleotides. It is part of OpenMS. Detailed information about NASE, including some applications, was published in Nature Communications.
This repository contains R code to generate sequence coverage visualisations for NASE search results. Given one or two NASE output file(s) in (RNA-variant) mzTab format, an HTML file is produced as output. Example plot:
Usage:
source("plot_coverage_full.R")
openms.chemistry.dir <- "..." # adjust path depending on your OpenMS installation
mztab1 <- read.mzTab("NASE_output1.mzTab")
mztab2 <- read.mzTab("NASE_output2.mzTab")
## insert optional filtering here...
html <- make.coverage.html(mztab1, mztab2)
cat(html, file="coverage_plot.html")See documentation in the code for more details.