!!!Caution work in progress!!!
library(bibliospec) knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE, results = "hide", fig.width = 7, fig.height = 4.5)
blib <- Blib() datdir <- "inst/singleProteomeDats/" files <- dir(datdir) files <- grep("*\\.dat$", files, value=TRUE) # blib$build(file.path(datdir,files), outfile = "inst/singleProteomeDats/All0_0.blib", cutoff=0.0) # blib$build(file.path(datdir,files), outfile = "inst/singleProteomeDats/All0_95.blib", cutoff=0.95) # # # blib$build(file.path(datdir,grep("Yeast",files,value=TRUE)), outfile = "inst/singleProteomeDats/YEAST0_95.blib", cutoff=0.95) # blib$build(file.path(datdir,grep("ecoli",files,value=TRUE)), outfile = "inst/singleProteomeDats/ECOLI0_95.blib", cutoff=0.95) # blib$build(file.path(datdir,grep("hela",files,value=TRUE)), outfile = "inst/singleProteomeDats/HELA0_95.blib", cutoff=0.95)
library(bibliospec) library(cdsw) dbfile <- file.path(path.package("cdsw"), "extdata/tripleProteomeBlib/ECOLI0_95.blib") All95 <- Bibliospec(dbfile) peaks95 <- All95$getSpectraMeta() peaks95 <- data.frame(mz = peaks95$precursorMZ, numpeaks = peaks95$numPeaks) ms2coutns95 <- rep(peaks95$mz, peaks95$numpeaks) par(mfrow=c(1,2)) h95 <- hist( peaks95$mz, breaks=400, xlab="MS1", main="" ) ms2h95 <- hist(ms2coutns95,breaks=400, xlab="MS2", ylab="MS2 peak frequency", main="")
mzStart <- 400 mzEnd <- 1100 nrWindows <- 20
\pagebreak
library(cdsw) cdsw <- Cdsw( peaks95$mz[peaks95$mz>mzStart&peaks95$mz < mzEnd], nbins=nrWindows, digits=1 ) cdsw$constant_breaks(digits = 1) cdsw$plot() cdsw$showCycle()
knitr::kable(cdsw$asTable())
cdsw$quantile_breaks(digits = 1) cdsw$plot() cdsw$showCycle()
knitr::kable(cdsw$asTable())
cdsw$sampling_breaks(maxwindow = 120,digits = 1,plot=TRUE) cdsw$plot() cdsw$showCycle()
knitr::kable(cdsw$asTable())
Equalizing for number of MS2 in each DIA map.
library(cdsw) cdsw <- Cdsw(ms2coutns95[ms2coutns95>mzStart& ms2coutns95 < mzEnd], nbins=nrWindows, digits=1 ) cdsw$constant_breaks(digits = 1) cdsw$plot() cdsw$showCycle()
knitr::kable(cdsw$asTable()) quantable::write.tab(cdsw$asTable(), file="d:/projects/p1000/tripleProteome/TripleProteomeWindows20Classic.txt")
knitr::kable(cdsw$optimizeWindows(plot=TRUE)) quantable::write.tab(cdsw$optimizeWindows(), file="d:/projects/p1000/tripleProteome/TripleProteomeWindows20ClassicOptimized.txt")
cdsw$quantile_breaks(digits = 1) cdsw$plot() cdsw$showCycle()
knitr::kable(cdsw$asTable())
cdsw$sampling_breaks(maxwindow = 120,digits = 1,plot=TRUE) cdsw$plot() cdsw$showCycle()
knitr::kable(cdsw$asTable()) quantable::write.tab(cdsw$asTable(), file="d:/projects/p1000/tripleProteome/TripleProteomeWindows20VariableContstrained.txt")
knitr::kable(cdsw$optimizeWindows(plot=TRUE)) quantable::write.tab(cdsw$optimizeWindows(), file="d:/projects/p1000/tripleProteome/TripleProteomeWindows20VariableContstrainedOptimized.txt")
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