Nothing
`make.par.file` <-
function(covariates, form, par.file="parameters.RData", root.dir=".", ...){
default.vals <- list(
add.norm = TRUE,
add.par = 0,
align.fcn = NA,
align.method = "spline",
base.dir = paste(root.dir, "/Baselines", sep=""),
bhbysubj = FALSE,
calc.all.peaks = FALSE,
cluster.constant = 10,
cluster.method = "ppm",
cor.thresh = 0.8,
FDR = 0.1,
FTICRMS.version = "0.8",
gengamma.quantiles = TRUE,
halve.search = FALSE,
isotope.dist = 7,
lrg.dir = paste(root.dir, "/Large_Peaks", sep=""),
lrg.file = "lrg_peaks.RData",
lrg.only = TRUE,
masses = NA,
max.iter = 20,
min.spect = 1,
neg.div = NA,
neg.norm.by = "baseline",
norm.peaks = "common",
norm.post.repl = FALSE,
num.pts = 5,
oneside.min = 1,
overwrite = FALSE,
par.file = "parameters.RData",
peak.dir = paste(root.dir, "/All_Peaks", sep=""),
peak.method = "parabola",
peak.thresh = 3.798194,
pre.align = FALSE,
pval.fcn = "default",
R2.thresh = 0.98,
raw.dir = paste(root.dir, "/Raw_Data", sep=""),
rel.conv.crit = TRUE,
repl.method = "max",
res.dir = paste(root.dir, "/Results", sep=""),
res.file = "analyzed.RData",
root.dir = ".",
sm.div = NA,
sm.norm.by = "baseline",
sm.ord = 2,
sm.par = 1e-11,
subtract.base = FALSE,
tol = 5e-8,
trans.method = "shiftedlog",
use.model = "lm",
zero.rm = TRUE
)
new.vals <- c(list(...), root.dir=root.dir, par.file=par.file)
for(i in names(default.vals)){
if(i %in% names(new.vals)){
assign(i, new.vals[[i]])
} else {
assign(i, default.vals[[i]])
}
}
tmp <- !(names(new.vals) %in% names(default.vals))
if(sum(tmp)==1){
warning(paste(names(new.vals)[tmp], "is not a valid parameter name"))
} else if(sum(tmp)==2){
warning(paste(paste(names(new.vals)[tmp], collapse=" and "),
"are not valid parameter names"))
} else if(sum(tmp)>2){
names(new.vals)[tmp][sum(tmp)] <- paste("and", names(new.vals)[tmp][sum(tmp)])
warning(paste(paste(names(new.vals)[tmp], collapse=", "),
"are not valid parameter names"))
}
save(list=setdiff(ls(), c("default.vals", "new.vals", "tmp", "i")),
file=paste(root.dir, "/", par.file, sep=""))
}
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