getVenn <- function(dataA, name_a, dataB, name_b, mz.thresh = 10,
time.thresh = 30, alignment.tool = NA, xMSanalyzer.outloc,
use.unique.mz = FALSE, plotvenn = TRUE, num_nodes = 2) {
dir.create(xMSanalyzer.outloc, showWarnings = FALSE)
plotvenn = FALSE
data_a <- as.data.frame(dataA)
data_b <- as.data.frame(dataB)
rm(dataA)
rm(dataB)
common <- {
}
commonA <- {
}
commonB <- {
}
############################################
if (use.unique.mz == TRUE) {
data_a <- find.Unique.mzs.sameset(dataA = data_a,
dataB = data_a, mz.thresh = mz.thresh, time.thresh = time.thresh,
alignment.tool = alignment.tool)
data_a <- data_a$uniqueA
# print(dim(data_a))
data_b <- find.Unique.mzs.sameset(dataA = data_b,
dataB = data_b, mz.thresh = mz.thresh, time.thresh = time.thresh,
alignment.tool = alignment.tool)
data_b <- data_b$uniqueA
}
# common<-find.Overlapping.mzs(data_a,data_b,mz.thresh,time.thresh=time.thresh,alignment.tool=alignment.tool)
# save(list=ls(),file='overlap.Rda')
common <- find.Overlapping.mzsvparallel(data_a, data_b,
mz.thresh, time.thresh = time.thresh, alignment.tool = alignment.tool,
num_nodes = num_nodes)
if (is.na(time.thresh) == FALSE) {
mznames = c("index.A", "mz.data.A", "time.data.A",
"index.B", "mz.data.B", "time.data.B", "time.difference")
} else {
mznames = c("index.A", "mz.data.A", "index.B", "mz.data.B")
}
if (length(common) > 0) {
# commonA<-data_a[c(common$index.A),]
# commonA<-unique(commonA)
# commonB<-data_b[c(common$index.B),]
# commonB<-unique(commonB)
# colnames(common)<-c('index.A','mz.data.A','index.B','mz.data.B')
colnames(common) <- mznames
} else {
num_common <- 0
commonA <- {
}
commonB <- {
}
}
return(list(common = common))
# ,'commonA'=commonA,'commonB'=commonB))
}
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