find.Unique.mzs.sameset <- function(dataA, dataB,
mz.thresh = 10, time.thresh = NA, alignment.tool = NA) {
print(dim(dataA))
data_a <- as.data.frame(dataA)
data_b <- as.data.frame(dataB)
data_a <- unique(data_a)
rm(dataA)
rm(dataB)
data_b <- unique(data_b)
com_mz_num = 1
unique_mz = {
}
ppm_v = {
}
rt_v = {
}
commat = {
}
col.names.dataA = colnames(data_a)
col.names.dataB = colnames(data_b)
if (is.na(alignment.tool) == FALSE) {
if (alignment.tool == "apLCMS") {
sample.col.start = 5
} else {
if (alignment.tool == "XCMS") {
sample.col.start = 9
col.names.dataA[1] = "mz"
col.names.dataA[2] = "time"
col.names.dataB[1] = "mz"
col.names.dataB[2] = "time"
colnames(data_a) = col.names.dataA
colnames(data_b) = col.names.dataB
}
}
} else {
# stop(paste('Invalid value for alignment.tool.
# Please use either \'apLCMS\' or \'XCMS\'',
# sep=''))
col.names.dataA[1] = "mz"
col.names.dataB[1] = "mz"
if (is.na(time.thresh) == FALSE) {
col.names.dataA[2] = "time"
col.names.dataB[2] = "time"
print("Using the 1st columns as \"mz\" and 2nd columsn as \"retention time\"")
} else {
print("Using the 1st columns as \"mz\"")
}
colnames(data_a) = col.names.dataA
colnames(data_b) = col.names.dataB
}
# data_a<-data_a[order(data_a$mz),]
# data_b<-data_b[order(data_b$mz),]
data_a <- as.data.frame(data_a)
data_b <- as.data.frame(data_b)
colnames(data_a) = col.names.dataA
colnames(data_b) = col.names.dataB
# create header for the matrix with common
# features
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")
}
overlap_res <- find.Overlapping.mzs(dataA = data_a,
dataB = data_b, mz.thresh, time.thresh, alignment.tool)
print(overlap_res)
filt_ind <- which(overlap_res$index.A != overlap_res$index.B)
if (length(filt_ind) > 0) {
uniqueA <- data_a[-c(filt_ind), ]
} else {
uniqueA <- data_a
}
return(list(uniqueA = uniqueA))
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.