msQCpipe {proteoQC} | R Documentation |
This function is designed to automate generating of target-decoy database, database searcing, post-processing and report generation.
msQCpipe(spectralist = NULL, fasta = "", outdir = "./", mode = "", miss = 2, enzyme = 1, varmod = NULL, fixmod = NULL, tol = 10, tolu = "ppm", itol = 0.6, itolu = "Daltons", threshold = 0.01, cpu = 0, xmx = 2, refine = TRUE, ntt = 1, ...)
spectralist |
A file contains the experiment design or a single mgf file |
fasta |
database file, must contain decoy sequences |
outdir |
output directory |
mode |
identification or quantification |
miss |
max miss clevage |
enzyme |
enzyme |
varmod |
Variable modifications are those which may or may not be present. |
fixmod |
Fixed modifications are applied universally, to every instance of the specified residue(s) or terminus. |
tol |
The error window on experimental peptide mass values |
tolu |
Units can be selected from: ppm, Daltons(also da or Da). |
itol |
Error window for MS/MS fragment ion mass values. |
itolu |
Units can be selected from: Daltons(also da or Da) |
threshold |
FDR value for PSM |
cpu |
Max number of cpu used |
xmx |
JAVA -Xmx |
refine |
Refine search for X!Tandem, default is TRUE. |
ntt |
Semi-tryptic, 1; fully-tryptic, 2. |
... |
Additional parameters passed to
|
A list which contains all of the information for data quality report generating
Bo Wen wenbo@genomics.cn
## Not run: library("rpx") px <- PXDataset("PXD000864") mgfs <- grep("mgf", pxfiles(px), value = TRUE) mgfs <- grep("-0[5-6]-[1|2]", mgfs, value=TRUE) mgffiles <- pxget(px, mgfs) library("R.utils") mgffiles <- sapply(mgffiles, gunzip) ## Generate the lightweight qc report, ## trim the mgf files to 1/10 of their size. 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) mgffiles <- sapply(mgffiles, trimMgf, overwrite = TRUE) fas <- pxget(px, "TTE2010.zip") fas <- unzip(fas) design <- system.file("extdata/PXD000864-design.txt", package = "proteoQC") read.table(design, header = TRUE) qcres <- msQCpipe(spectralist = design, fasta = fas, outdir = "./qc", miss = 0, enzyme = 1, varmod = 2, fixmod = 1, tol = 10, itol = 0.6, cpu = 2, mode = "identification") ## End(Not run)