Hi Tom
It looks as if you are reading in genepix files. I believe the format for the
start lines includes a second line to say how many lines to skip. Something
like this, specifying 27 lines to skip:
ATF 1
27 43
Type=GenePix Results 1.4
DateTime=2003/11/14 17:18:30
If so here is a function I use to do what you want to do. If your files have a
different format then you need to modify how you set the number of lines to
skip.
# Preprocess the genepix files - strip off first header lines
dopix<-function(genepixfiles, workingdir) {
pre<-"Pre"
# Read in each genepix file, strip unwanted rows and write out again
for (pixfile in genepixfiles) {
pixfileout<-paste(workingdir, pre, basename(pixfile), sep="")
secondline<-read.table(pixfile, skip=1, nrows=1)
skiplines<-as.numeric(secondline[1]) + 2
outdf<-read.table(pixfile, header=T, skip=skiplines, sep="\t")
write.table(outdf, file=pixfileout, sep="\t", row.names=FALSE)
}
}
Regards
John Seers
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tom Cohen
Sent: 03 August 2007 13:04
To: r-help@stat.math.ethz.ch
Subject: Re: [R] problem with reading data files with different numbers oflines
to skip
Thanks to Ted and Gabor for your response.
I apology for not being clear with my previous description of the problem. I
tried with your suggestions using readLines but couldn't make it work. I now
explain the problem in more details and hope that you can help me out.
I have 30 data files, where some of them have 33 lines and the rests have 31
lines that I want to skip (examples below with bold text). That is, I only want
to keep the lines start from
Block Column Row Name ID
I read in the data files with a loop like below, the problem is how do I tell
the loop to skip 31 lines in some data files and 33 in the rests ?
> for (i in 1:num.files) {
> a<-read.table(file=data[i],
> ,header=T,skip=31,sep='\t',na.strings="NA") }
Thanks for your help,
Tom
# 33 lines to skip
Type=GenePix Results 3 DateTime=2006/10/20
13:35:11 Settings=
GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-human-pep2.gal PixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-2.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-2.s1.jpg StdDev=Type 1
RatioFormulations=W1/W2 (635/) FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1940, 3670
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B [84948]
FocusPosition=0 Temperature=30.2
LinesAveraged=1
Comment= PMTGain=600
ScanPower=100 LaserPower=3.36
Filters=<Empty> ScanRegion=56,136,2123,6532
Supplier=Genetix Ltd. ArrayerSoftwareName=MicroArraying
ArrayerSoftwareVersion=QSoft XP Build 6450 (Revision 131)
Block Column Row Name ID X Y Dia. F635 Median F635 Mean 1 1 1
IgG-human none 2390 4140 200 301 317 1 2 1 >PGDR_HUMAN (P09619)
AHASDEIYEIMQK 2630 4140 200 254 250 1 3 1 >ML1X_HUMAN (Q13585)
AIAHPVSDDSDLP 2860 4140 200 268 252
1000 more rows....
# 31 lines to skip
ATF 1.0 29 41
Type=GenePix Results 3 DateTime=2006/10/20 13:05:20
Settings= GalFile=G:\Avdelningar\viv\translational
immunologi\Peptide-arrays\Gal-files\742-s2.gal PixelSize=10
Wavelengths=635
ImageFiles=M:\Peptidearrays\061020\742-4.tif 1
NormalizationMethod=None NormalizationFactors=1
JpegImage=C:\Documents and Settings\Shahnaz Mahdavifar\Skrivbord\Human
pep,742\742-4.s2.jpg StdDev=Type 1
RatioFormulations=W1/W2 (635/) FeatureType=Circular
Barcode= BackgroundSubtraction=LocalFeature
ImageOrigin=560, 1360 JpegOrigin=1950, 24310
Creator=GenePix Pro 6.0.1.25 Scanner=GenePix 4000B [84948]
FocusPosition=0
Temperature=28.49 LinesAveraged=1
Comment= PMTGain=600 ScanPower=100
LaserPower=3.32 Filters=<Empty>
ScanRegion=56,136,2113,6532 Supplier=
Block Column Row Name ID X Y Dia. F635 Median F635 Mean 1 1 1
IgG-human none 2370 24780 200 133 175 1 2 1 >PGDR_HUMAN (P09619)
AHASDEIYEIMQK 2600 24780 200 120 121 1 3 1 >ML1X_HUMAN (Q13585)
AIAHPVSDDSDLP 2840 24780 200 120 118
1000 more rows....
[EMAIL PROTECTED] skrev:
On 02-Aug-07 21:14:20, Tom Cohen wrote:
> Dear List,
>
> I have 30 data files with different numbers of lines (31 and 33) that
> I want to skip before reading the files. If I use the skip option I
> can only choose either to skip 31 or 33 lines. The data files with 31
> lines have no blank rows between the lines and the header row. How can
> I read the files without manually checking which files have 31
> respectively 33 lines ? The only text line I want to keep is the header.
>
> Thamks for your help,
> Tom
>
>
> for (i in 1:num.files) {
> a<-read.table(file=data[i],
> ,header=T,skip=31,sep='\t',na.strings="NA")
>
> }
Apologies, I misunderstood your description in my previous response (I thought
that the total number of lines in one of your files was either 31 or 33, and
you wanted to know which was which).
I now think you mean that there are either 0 (you want to skip 31) or 2 (you
want to skip 33) blank lines in the first 33, and then you want the remainder
(aswell as the header). Though it's still not really clear ...
You can find out how many blank lines there are in the first 33 with
> sum(cbind(readLines("~/00_junk/temp.tr", 33))=="")
and then choose how many lines to skip.
Best wishes,
Ted.
--------------------------------------------------------------------
E-Mail: (Ted Harding)
Fax-to-email: +44 (0)870 094 0861
Date: 03-Aug-07 Time: 00:11:21
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