runTandem {proteoQC} | R Documentation |
Run X!Tandem
run X!Tandem
runTandem(spectra = "", fasta = "", outdir = "./", outprefix = "", cpu = 1, enzyme = 1, xmx = 2, varmod = NULL, fixmod = NULL, refine = TRUE, ntt = 1, tol = 10, tolu = "ppm", itol = 0.6, itolu = "Daltons", miss = 1)
spectra |
MS/MS peak list file |
fasta |
database file |
outdir |
output directory |
outprefix |
output file prefix |
cpu |
The number of CPU used for X!Tandem |
enzyme |
The ID of enzyme used for database searching.
See |
xmx |
Set for parameter of "Java -Xmx". |
varmod |
Variable modifications used for database searching.
See |
fixmod |
Fixed modifications used for database searching.
See |
refine |
Refine search, default is TRUE |
ntt |
Default is 1 |
tol |
The error window on experimental peptide mass values |
tolu |
Units can be selected from: ppm, Daltons. |
itol |
Error window for MS/MS fragment ion mass values. |
itolu |
Units can be selected from: Daltons |
miss |
Max miss clevage |
a file path
Bo Wen wenbo@genomics.cn