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55 lines
2.2 KiB
R
55 lines
2.2 KiB
R
##################################################
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################### muxd2df ######################
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##################################################
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muxd2df <- function(uxdfile, range.descriptor) {
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# Function that reads an UXD file which contains several ranges
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# (created in a programmed run, for example)
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# Arguments
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# :: uxdfile (filename with extension)
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# :: range.descriptor (an array with as many elements as
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# there are ranges in the uxdfile)
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# Returns: dataframe with 3 columns
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cchar <- "[;_]" #regexpr matching the comment characters used in Bruker's UXD
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cdata <- "[0-9]" #regexpr matching one character of any digit
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# Create filenames for the output # no longer used, return dataframe instead
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#datafile <- paste(uxdfile,"-",range.descriptor,".data",sep="")
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# Read the input multirange file
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ufile <- file(uxdfile, "r")
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f <- readLines(ufile, n=-1) #read _all_ lines from UXD file
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close(ufile)
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# This way we identify data rows by looking for numeric characters.
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#wh <- regexpr("[0-9]", f)
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# This way we identify header rows
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# Later we will assume that all other rows are data
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wh <- regexpr(cchar, f)
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mh <- wh[1:length(wh)] # this gives you the corresponding index vector
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# the value of each element corresponds to the position of the regexp match.
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# value = 1 means the first character of the row is cchar (row is header)
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# value =-1 means no cchar occur on the row (row is data)
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#length(mh[mh == -1]) #total number of datarows in uxdfile
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#mh[mh > 1 | mh < 0] <- 0 #set all header-rows to zero (just to make things easier)
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i <- seq(1, length(mh) - 1, 1)
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j <- seq(2, length(mh), 1)
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starts <- which(mh[i] == 1 & mh[j] != 1) + 1 #start indices
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ends <- which(mh[i] != 1 & mh[j] == 1) #end indices, except the last
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ends <- c(ends, length(mh)) #fixed the last index of ends
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ff <- data.frame(NULL)
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for (s in 1:length(range.descriptor)) {
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zz <- textConnection(f[starts[s]:ends[s]], "r")
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ff <- rbind(ff, data.frame(range.descriptor[s],
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matrix(scan(zz, what = numeric()), ncol=2, byrow=T)))
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close(zz)
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}
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names(ff) <- c("sampleid", "angle", "intensity")
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# Return dataframe
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ff
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}
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