Comments (3)
Map columns from RawDiag to CV terms.
c("filename", "scanNumber", "StartTime", "BasePeakMass",
"BasePeakIntensity", "TIC", "ScanType", "CycleNumber",
"MSOrder", "MassAnalyzer", "PrecursorMass", "ChargeState",
"IonInjectionTimems", "FTResolution", "MasterScanNumber",
"LMCorrection", "ElapsedScanTimesec", "transient", "AGC",
"AGCMode", "PrescanMode")
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo
from rawdiag.
I will most likely not manage to do this before 15th of May (application deadline).
from rawdiag.
the code snippet below should do the job
#' mzR reader method
#'
#' @param object an mzR object
#'
#' @return an \code{\link{rawDiag}} object
#' @author Christian Panse <[email protected]>, Witold E.Wolski <[email protected]>
#' @example
#'
#' library(mzR)
#' mzmlFilename <- "PXD006932/Exp3A/20161213_NGHF_DBJ_SA_Exp3A_HeLa_1ug_15min_15000_01.mzML"
#' S <- as.rawDiag.mzR(openMSfile(mzmlFilename))
#'
as.rawDiag.mzR <- function(object){
#time.start <- Sys.time()
runInfo <- runInfo(object)
rv <- lapply(1:runInfo$scanCount,
function(x){data.frame(header(object, x))})
rv <- bind_rows(rv)
#time.end <- Sys.time()
#message(time.start - time.end)
rv <- rv[, c('acquisitionNum', 'retentionTime', 'basePeakMZ',
'basePeakIntensity', 'totIonCurrent', 'msLevel', 'precursorMZ',
'precursorCharge')]
colnames(rv) <- c('scanNumber', 'StartTime', 'BasePeakMass',
'BasePeakIntensity', 'TIC', 'MSOrder', 'PrecursorMass',
'ChargeState')
rv$filename <- basename(fileName(object))
as.rawDiag(rv)
}
from rawdiag.
Related Issues (20)
- plot.peaklist function does not allow to overwrite title and y- n xlabels
- R 4.0.2 - Error: `x` must be a vector, not a `data.frame/rawDiag` object. HOT 3
- Problems reading Meta Data from QExactive HF / HFX Instruments HOT 28
- Reading Analag Traces from RawFiles HOT 7
- Read additional Infos from Raw Files (Status Log, Tune Method) etc. HOT 10
- create unit test for `read.raw.info()`
- Cannot find dependency "Spectra" HOT 2
- .computeBestPeptideSpectrumMatch function HOT 11
- Installation of new RawFileReader files HOT 19
- Error in source(tfo) : negative length vectors are not allowed HOT 15
- replace `warning` with `message`
- Deprecation messages for read.XIC() and readScans() HOT 1
- `funs()` was deprecated in dplyr 0.8.0.
- Error in FUN(left, right) : non-numeric argument to binary operator in `PlotCycleTime` HOT 2
- issues with tempfile opening
- I am trying to run read.raw, but it returns an error HOT 1
- [Extra feature that would be nice] Using m/z / RT values for QCs rather peptides
- protViz 0.6.8 required prior to install rawDiag on R.4.0.5
- Package "mardown" and "plyr" have to be installed so the ShinyApp works
- Problems with the read.raw()
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from rawdiag.