select portion of text file using R
On 27/04/2015 5:20 PM, Luigi Marongiu wrote:
Dear Duncan, thank you for your reply, I tried to read the file using skip and nrows but it did not work.
What does that mean? We might be able to be more help if you tell us what happened when you tried the code below.
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,
That's a strange entry, in conflict with the entry below...
dec=".",
sep="\t",
skip = 30,
nrows = 17281,
row.names = 1:17281
... i.e. here. If you don't have row names in the file, there's no need to specify them numerically: that would be the default. So I'd drop *both* cases where you give the row.names argument. Also, I may have counted wrong, but it looks to me that the line with the column headings is line 32, so you should have skip = 31. Duncan Murdoch
) 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 <murdoch.duncan at gmail.com> wrote:
On 20/04/2015 3:28 AM, Luigi Marongiu wrote:
Dear all, I have a flat file (tab delimited) derived from an excel file which is subdivided in different parts: a first part is reporting metadata, then there is a first spreadsheet indicated by [ ], then the actual data and the second spreadsheet with the same format [ ] and then the data. How can I import such file using for instance read.table()?
read.table() by itself can't recognize where the data starts, but it has arguments "skip" and "nrows" to control how much gets read. If you don't know the values for those arguments, you can use readLines() to read the entire file, then use grep() to recognize your table data, and either re-read the file, or just extract those lines and read from them as a textConnection. Duncan Murdoch
Many thanks regards Luigi Here is a sample of the file: * Experiment Barcode = * Experiment Comments = * Experiment File Name = F:\array 59 * Experiment Name = 2015-04-13 171216 * Experiment Run End Time = 2015-04-13 18:07:57 PM PDT ... [Amplification Data] Well Cycle Target Name Rn Delta Rn 1 1 Adeno 1-Adeno 1 0.820 -0.051 1 2 Adeno 1-Adeno 1 0.827 -0.042 1 3 Adeno 1-Adeno 1 0.843 -0.025 1 4 Adeno 1-Adeno 1 0.852 -0.015 1 5 Adeno 1-Adeno 1 0.858 -0.008 1 6 Adeno 1-Adeno 1 0.862 -0.002 ... [Results] Well Well Position Omit Sample Name Target Name Task Reporter Quencher RQ RQ Min RQ Max CT Ct Mean Ct SD Quantity Delta Ct Mean Delta Ct SD Delta Delta Ct Automatic Ct Threshold Ct Threshold Automatic Baseline Baseline Start Baseline End Efficiency Comments Custom1 Custom2 Custom3 Custom4 Custom5 Custom6 NOAMP EXPFAIL 1 A1 false P17 Adeno 1-Adeno 1 UNKNOWN FAM NFQ-MGB Undetermined false 0.200 true 3 44 1.000 N/A N Y 2 A2 false P17 Adeno 40/41 EH-AIQJCT3 UNKNOWN FAM NFQ-MGB Undetermined
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