readXICs | R Documentation |
Extracts XICs of a given mass vector
readXICs(
rawfile,
masses,
tol = 10,
mono = if (Sys.info()["sysname"] %in% c("Darwin", "Linux")) TRUE else FALSE,
exe = .rawDiagAssembly()
)
rawfile |
the file name |
masses |
a vector of masses |
tol |
tolerance in ppm |
mono |
if the mono enviroment should be used. |
exe |
the exe file user by mono |
list of XIC objects
# Example 1: extract iRT peptides
iRTpeptide <- c("LGGNEQVTR", "YILAGVENSK", "GTFIIDPGGVIR", "GTFIIDPAAVIR",
"GAGSSEPVTGLDAK", "TPVISGGPYEYR", "VEATFGVDESNAK",
"TPVITGAPYEYR", "DGLDAASYYAPVR", "ADVTPADFSEWSK",
"LFLQFGAQGSPFLK")
library(protViz)
# 2Hplus
(mZ <- (parentIonMass(iRTpeptide) + 1.008) / 2)
## Not run:
f <- "ftp://massive.ucsd.edu/MSV000086542/raw/20181113_010_autoQC01.raw"
rawfile <- file.path(cachedir <- tools::R_user_dir("rawrr", which='cache'), "20181113_010_autoQC01.raw")
if (!dir.exists(cachedir)) { dir.create(cachedir, recursive = TRUE) }
if (!file.exists(rawfile)) { download.file(f, rawfile) }
X <-readXICs(rawfile, masses=mZ)
## End(Not run)
(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))
RAW <- read.raw(rawfile)
# not meaning full but proof-of-concept
X <- readXICs(rawfile, masses=unique(RAW$PrecursorMass), tol=1000)
plot.XIC(X)
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