sgibb’s gists

sgibb / fwhm.R

Created October 18, 2012 19:33

Calculate FWHM.

	fwhm <- function(spectrum, peaks) {

	## work horse
	.fwhm <- function(spectrum, i) {
	n <- length(spectrum)
	left <- ifelse(i <= 1, 1, i)
	right <- ifelse(i >= n, n, i)

	hm <- spectrum@intensity[i]/2

sgibb / importBrukerXml.R

Created February 12, 2013 21:18

quick & dirty approach to import Bruker xml files.

	## code to import peaks from Bruker xml files

	importBrukerXml <- function(file) {
	require("MALDIquant")

	## read file
	r <- readLines(file)

	## remove useless stuff
	r <- gsub(pattern="^.<ms_peaks>\|</ms_peaks>.$", replacement="", x=r)

sgibb / server.R

Last active December 18, 2015 04:28

give shiny a try; to run this example: `install.packages("shiny"); library("shiny"); runGist("5725234")`

	library("shiny")

	library("MALDIquant")

	data("fiedler2009subset")

	shinyServer(function(input, output) {

	output$plotBaseline <- renderPlot({
	plot(fiedler2009subset[[1]])

sgibb / server.R

Last active June 16, 2021 16:39

shiny app that provides a basic MALDIquant workflow. `library("shiny"); runGist("5751429")`

	library("shiny")

	library("MALDIquant")
	library("MALDIquantForeign")

	options(shiny.maxRequestSize=200*1024^2)

	data("fiedler2009subset")

	convertYlim <- function(lim, fun) {

sgibb / avgpeaks.R

Created June 15, 2013 16:49

find individual peaks from an average spectrum

	library("MALDIquant")

	data("fiedler2009subset")

	## preprocessing
	spectra <- transformIntensity(fiedler2009subset, sqrt)
	spectra <- transformIntensity(spectra, savitzkyGolay)
	spectra <- removeBaseline(spectra)
	peaks <- detectPeaks(spectra)

sgibb / binning.R

Created June 25, 2013 22:31

demonstrate differences between strict/relaxed binning

	library("MALDIquant")

	#' create toy example
	p <- c(p1=createMassPeaks(mass=c(1, 1.5, 10), intensity=c(1, 2, 1),
	metaData=list(name="p1")),
	p2=createMassPeaks(mass=c(0.9, 10.1), intensity=c(1, 1),
	metaData=list(name="p2")),
	p3=createMassPeaks(mass=c(1.1, 9.9), intensity=c(1, 1),
	metaData=list(name="p3")))

sgibb / Bioconductor-patched.sty

Created July 22, 2013 20:45

BiocStyle + knitr; try `library("knitr"); library("BiocStyle"); knit("knitr.Rnw"); tools::texi2pdf("knitr.tex")`

	\NeedsTeXFormat{LaTeX2e}
	\ProvidesPackage{Bioconductor}[2013/07/01 Bioconductor vignette style]

	%% -I would wish to know how to make this work-
	%% \DeclareOption{pdftitle}{\PassOptionsToPackage{pdftitle}{hyperref}}
	%% \DeclareOption{pdfauthor}{\PassOptionsToPackage{pdfauthor}{hyperref}}
	%% \ExecuteOptions{pdftitle,pdfauthor}
	%% \ProcessOptions

	\PassOptionsToPackage{usenames,dvipsnames}{color}

sgibb / convertFile.R

Created September 9, 2013 17:11

convert a file from one encoding to another one

	convertFile <- function(inputFile, outputFile,
	fromEncoding="UTF-8", toEncoding="ASCII") {
	stopifnot(file.exists(inputFile))
	input <- readLines(inputFile, encoding=fromEncoding)
	output <- iconv(input, from=fromEncoding, to=toEncoding)
	return(writeLines(output, outputFile))
	}

sgibb / createNetCdf.R

Last active January 4, 2016 17:19

Create a tiny NetCdf example file

	library("RNetCDF")

	nc <- create.nc("tiny.cdf")

	dim.def.nc(nc, "scan_number", 2)
	dim.def.nc(nc, "point_number", 10, unlim=TRUE)

	var.def.nc(nc, "scan_index", "NC_INT", "scan_number")
	var.def.nc(nc, "point_count", "NC_INT", "scan_number")
	var.def.nc(nc, "scan_acquisition_time", "NC_DOUBLE", "scan_number")

sgibb / findMSeEMRTs.R

Created February 28, 2014 23:00

MWE to demonstrate the speed improvement of findMSeEMRTs2

	library("synapter")
	library("synapterdata")

	## map some private functions to global NAMESPACE
	doHDMSePredictions <- synapter:::doHDMSePredictions
	error.ppm <- synapter:::error.ppm
	findMSeEMRTs <- synapter:::findMSeEMRTs

	###########################################################################
	## some boring stuff to prepare the Synapter object

Sebastian Gibb sgibb