select portion of text file using R

Hi Luigi

I think there may be problems with \t being equivalent to tab chr(9)

Therefore try

xlines <-
readLines(textConnection("* Block Type = Array Card Block
* Calibration Background is expired = No
* Calibration Background performed on = 2014-12-02 11:27:49 AM PST
* Calibration FAM is expired = No
* Calibration FAM performed on = 2014-12-02 12:00:20 PM PST
* Calibration ROI is expired = No
* Calibration ROI performed on = 2014-12-02 11:20:40 AM PST
* Calibration ROX is expired = No
* Calibration ROX performed on = 2014-12-02 12:11:21 PM PST
* Calibration Uniformity is expired = No
* Calibration Uniformity performed on = 2014-12-02 11:43:43 AM PST
* Calibration VIC is expired = No
* Calibration VIC performed on = 2014-12-02 11:51:59 AM PST
* Chemistry = TAQMAN
* Experiment Barcode =
* Experiment Comments =
* Experiment File Name = F:\2015-04-13 Gastro array 59 Luigi - plate 3.eds
* Experiment Name = 2015-04-13 171216
* Experiment Run End Time = 2015-04-13 18:07:57 PM PDT
* Experiment Type = Comparative C? (??C?)
* Experiment User Name =
* Instrument Name = 278882033
* Instrument Serial Number = 278882033
* Instrument Type = ViiA 7
* Passive Reference = ROX
* Quantification Cycle Method = Ct
* Signal Smoothing On = false
* Stage/ Cycle where Analysis is performed = Stage 3, Step 2
Well  Cycle   Target  Name  Rn
  1   1   Adeno 1   0.82
  1   2   Adeno 1   0.93
  2   1   Adeno 2   0.78") )
xlines = sub("^\\*.*$","", xlines)
xlines = xlines[nchar(xlines)>0]
xlines = sub("^[[:space:]]+","", xlines)
xlines = xlines[-1]
datc = data.frame(do.call(rbind, lapply(xlines, function(x) unlist(strsplit(x, "[[:space:]]+")))))
names(datc) = c("Well","Cycle","Target","Name","Rn")
dat = datc
for (j in c(1,2,4,5)) dat[,j] = as.numeric(dat[,j])

Regards

Duncan

Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Luigi Marongiu
Sent: Tuesday, 28 April 2015 07:20
To: Duncan Murdoch; r-help
Subject: Re: [R] select portion of text file using R

Dear Duncan,
thank you for your reply,
I tried to read the file using skip and nrows but it did not work.
Here i am pasting the code I wrote and the head of the file i need to
read. Probably the error is due to the fact that the column "well" has
duplication, but how can i add a row column with unique row names? How
can I overcome this error?
Best regards
Luigi

CODE
raw.data<-read.table(
      mydata,
      header=TRUE,
      row.names=31,
      dec=".",
      sep="\t",
      skip = 30,
      nrows = 17281,
      row.names = 1:17281
    )

HEAD OF MYDATA
* Block Type = Array Card Block
* Calibration Background is expired = No
* Calibration Background performed on = 2014-12-02 11:27:49 AM PST
* Calibration FAM is expired = No
* Calibration FAM performed on = 2014-12-02 12:00:20 PM PST
* Calibration ROI is expired = No
* Calibration ROI performed on = 2014-12-02 11:20:40 AM PST
* Calibration ROX is expired = No
* Calibration ROX performed on = 2014-12-02 12:11:21 PM PST
* Calibration Uniformity is expired = No
* Calibration Uniformity performed on = 2014-12-02 11:43:43 AM PST
* Calibration VIC is expired = No
* Calibration VIC performed on = 2014-12-02 11:51:59 AM PST
* Chemistry = TAQMAN
* Experiment Barcode =
* Experiment Comments =
* Experiment File Name = F:\2015-04-13 Gastro array 59 Luigi - plate 3.eds
* Experiment Name = 2015-04-13 171216
* Experiment Run End Time = 2015-04-13 18:07:57 PM PDT
* Experiment Type = Comparative C? (??C?)
* Experiment User Name =
* Instrument Name = 278882033
* Instrument Serial Number = 278882033
* Instrument Type = ViiA 7
* Passive Reference = ROX
* Quantification Cycle Method = Ct
* Signal Smoothing On = false
* Stage/ Cycle where Analysis is performed = Stage 3, Step 2

[Amplification Data]

Well \tCycle \tTarget \tName \tRn
\t1 \t1 \tAdeno 1 \t0.82
\t1 \t2 \tAdeno 1\ \t0.93
...
\t2 \t1 \tAdeno 2 \t0.78
...

On Mon, Apr 20, 2015 at 12:17 PM, Duncan Murdoch

select portion of text file using R

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