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Unverified Commit a7ef66fd authored by Todor Kondic's avatar Todor Kondic
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api: Remove set column during data extraction

* R/api.R (extr_data): An unecessary set column was removed from the
m$extr$ms table to avoid possible confusion. Extraction deals with
unique masses, so this column listed only the first set (in comp
table) that contained a particular mass. Later, during the prescreen
stage the set is coming back directly from the comp table.
parent c03a085d
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...@@ -246,6 +246,7 @@ extr_data <- function(m) { ...@@ -246,6 +246,7 @@ extr_data <- function(m) {
## Reduce the comp table to only unique masses (this is because ## Reduce the comp table to only unique masses (this is because
## different sets can have same masses). ## different sets can have same masses).
m$out$tab$data <- m$out$tab$comp[,head(.SD,1),by=c('adduct','tag','ID')] m$out$tab$data <- m$out$tab$comp[,head(.SD,1),by=c('adduct','tag','ID')]
m$out$tab$data[,set:=NULL] #This column is meaningless now.
files <- m$out$tab$data[,unique(Files)] files <- m$out$tab$data[,unique(Files)]
allCEs <- do.call(c,args=lapply(files,function(fn) { allCEs <- do.call(c,args=lapply(files,function(fn) {
z <- MSnbase::readMSData(files=fn,msLevel = c(1,2),mode="onDisk") z <- MSnbase::readMSData(files=fn,msLevel = c(1,2),mode="onDisk")
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