Nothing
library("msQC")
trimMgf <- function(f, m = 1/10, overwrite = FALSE) {
message("Reading ", f)
x <- readLines(f)
beg <- grep("BEGIN IONS", x)
end <- grep("END IONS", x)
n <- length(beg)
message("Sub-setting to ", m)
i <- sort(sample(n, floor(n * m)))
k <- unlist(mapply(seq, from = beg[i], to = end[i]))
if (overwrite) {
unlink(f)
message("Writing ", f)
writeLines(x[k], con = f)
return(f)
} else {
g <- sub(".mgf", "_small.mgf", f)
message("Writing ", g)
writeLines(x[k], con = g)
return(g)
}
}
set.seed(1)
trimMgf("Thermo_Hela_PRTC_1.mgf")
trimMgf("Thermo_Hela_PRTC_2.mgf")
trimMgf("Thermo_Hela_PRTC_3.mgf")
qcres <- msQCpipe(spectralist = "design_small.txt",
fasta = "swissprot_human_canonical_19_09_12.fasta",
outdir = "./qc",
miss = 0,
enzyme = 1, varmod = 2, fixmod = 1,
tol = 10, itol = 0.6, cpu = 2,
mode = "identification")
unlink("./qc/database/target_decoy.fasta")
unlink("./qc/result/*_xtandem.xml")
## reportHTML("./qc")
## unlink("./qc/report/*")
## unlink("./qc/qc_report.*")
zip("qc.zip", "qc")
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.