I'm trying to export a large data frame to a text file for permanent storage. The only thing I could find was the treeglia Package but that didn't work. Any suggestions? Thanks! Christina D Smith PhD Student, GRA Statistics Department Kansas State University
Look at ?write.table. Also, the data import/export manual on the r-project website is quite useful. Sean On Feb 18, 2005, at 12:32 PM, Christina D Smith wrote:> I'm trying to export a large data frame to a text file for permanent > storage. The only thing I could find was the treeglia Package but that > didn't work. Any suggestions? > Thanks! > > Christina D Smith > PhD Student, GRA > Statistics Department > Kansas State University > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html
Did you try "write.table"? If yes, what do you see as its
deficiencies?
spencer graves
Christina D Smith wrote:
>I'm trying to export a large data frame to a text file for permanent
>storage. The only thing I could find was the treeglia Package but that
>didn't work. Any suggestions?
>Thanks!
>
>Christina D Smith
>PhD Student, GRA
>Statistics Department
>Kansas State University
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
>
1. Did you work the example at the end of the "write.table" help
file? In R 2.0.1, this is:
write.table(x, file = "foo.csv", sep = ",", col.names =
NA)
This should create a file "foo.csv" in the working directory. To
find the working directory, use "getwd()"; to set it, use
"setwd(...)".
When you do this, can you find "foo.csv"?
2. I tried the command in your email:
>write.table(temp.data.data, file = "c:\Current Work")
I got a file "Current Work" (with no *.txt or other extension) in
"C:\".
3. You need to be careful with "\" in text strings, because it is
an
R escape character. For example, the following modification of your
example produced an error:
> write.table(temp.data.data, file = "c:\the Work")
Error in file(file, ifelse(append, "a", "w")) :
unable to open connection
In addition: Warning message:
cannot open file `c: he Work'
This occurs because "\t" is a tab character.
4. If you wanted a file called, say, "temp.data.data.txt" in
"c:\Current Work", you need something like the following:
write.table(temp.data.data,
file = "c:\\Current Work\\temp.data.data.txt")
Since "\" is the escape character in R, to get "\"
retained in the
character string, you need to use "\\"; "/" is accepted as
a substitute
for "\\".
hope this helps.
spencer graves
Christina D Smith wrote:
>I'm not sure. The following code gives me no errors:
>write.table(temp.data.data, file = "c:\Current Work")
>Yet no new file is created.
>Christy
>
>Quoting Spencer Graves <spencer.graves at pdf.com>:
>
###################
Did you try "write.table"? If yes, what do you see as its
deficiencies?
spencer graves
Christina D Smith wrote:
>I'm trying to export a large data frame to a text file for permanent
>storage. The only thing I could find was the treeglia Package but that
>didn't work. Any suggestions?
>Thanks!
>
>Christina D Smith
>PhD Student, GRA
>Statistics Department
>Kansas State University
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
>
Dear group, apologies for asking a simple question. I have a file where the data looks like this: Probe Intensity 0:0 501.0 1:0 17760.5 2:0 511.0 3:0 18468.3 4:0 199.8 5:0 508.0 6:0 17241.8 7:0 507.5 8:0 17910.0 9:0 482.5 10:0 17480.3 11:0 434.0 12:0 17631.3 13:0 444.8 14:0 17423.0 15:0 505.3 16:0 16693.0 17:0 438.5 18:0 16920.0 19:0 491.3 20:0 16878.0 21:0 486.3 22:0 16582.0 23:0 483.8 24:0 16694.8 25:0 452.3 26:0 16221.5 27:0 438.3 28:0 17119.8 29:0 455.5 30:0 16579.0 31:0 424.5 32:0 16691.3 33:0 472.0 My question is how do I know the distribution of the intensities. My aim is to find out the number of intensities or probes that fall in a certain range. For example 500 probes has intensities ranging from 50 to 150. 300 probes has intensities ranging from 151-250 I have no clue how to do it for 500,000 probes. Can any one please help doing it in R. thanks and apologies again srini
Srini You should probably look at ?hist. If you look at the "value" section, you will see that you can get the information you want from the values returned from hist. If these are microarray probes and intensities, there may be specific methods for visualizing the data available from the bioconductor project (www.bioconductor.org). Hope this helps, Sean ----- Original Message ----- From: "Srinivas Iyyer" <srini_iyyer_bio at yahoo.com> To: "Rhelp" <r-help at stat.math.ethz.ch> Sent: Monday, February 21, 2005 6:21 PM Subject: [R] Distribution> Dear group, > apologies for asking a simple question. I have a file > where the data looks like this: > Probe Intensity > 0:0 501.0 > 1:0 17760.5 > 2:0 511.0 > 3:0 18468.3 > 4:0 199.8 > 5:0 508.0 > 6:0 17241.8 > 7:0 507.5 > 8:0 17910.0 > 9:0 482.5 > 10:0 17480.3 > 11:0 434.0 > 12:0 17631.3 > 13:0 444.8 > 14:0 17423.0 > 15:0 505.3 > 16:0 16693.0 > 17:0 438.5 > 18:0 16920.0 > 19:0 491.3 > 20:0 16878.0 > 21:0 486.3 > 22:0 16582.0 > 23:0 483.8 > 24:0 16694.8 > 25:0 452.3 > 26:0 16221.5 > 27:0 438.3 > 28:0 17119.8 > 29:0 455.5 > 30:0 16579.0 > 31:0 424.5 > 32:0 16691.3 > 33:0 472.0 > > > My question is how do I know the distribution of the > intensities. My aim is to find out the number of > intensities or probes that fall in a certain range. > > For example 500 probes has intensities ranging from 50 > to 150. > > 300 probes has intensities ranging from 151-250 > > I have no clue how to do it for 500,000 probes. Can > any one please help doing it in R. > > thanks and apologies again > > srini > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html >
Have you considered "qqnorm" or "hist"? If yes,
"PLEASE do read
the posting guide! http://www.R-project.org/posting-guide.html". It
might help you phrase your question so you are more likely to get a
useful response -- and it might help you get the answer for yourself
without waiting for someone to reply.
hope this helps. spencer graves
Srinivas Iyyer wrote:
>Dear group,
>apologies for asking a simple question. I have a file
>where the data looks like this:
>Probe Intensity
>0:0 501.0
>1:0 17760.5
>2:0 511.0
>3:0 18468.3
>4:0 199.8
>5:0 508.0
>6:0 17241.8
>7:0 507.5
>8:0 17910.0
>9:0 482.5
>10:0 17480.3
>11:0 434.0
>12:0 17631.3
>13:0 444.8
>14:0 17423.0
>15:0 505.3
>16:0 16693.0
>17:0 438.5
>18:0 16920.0
>19:0 491.3
>20:0 16878.0
>21:0 486.3
>22:0 16582.0
>23:0 483.8
>24:0 16694.8
>25:0 452.3
>26:0 16221.5
>27:0 438.3
>28:0 17119.8
>29:0 455.5
>30:0 16579.0
>31:0 424.5
>32:0 16691.3
>33:0 472.0
>
>
>My question is how do I know the distribution of the
>intensities. My aim is to find out the number of
>intensities or probes that fall in a certain range.
>
>For example 500 probes has intensities ranging from 50
>to 150.
>
>300 probes has intensities ranging from 151-250
>
>I have no clue how to do it for 500,000 probes. Can
>any one please help doing it in R.
>
>thanks and apologies again
>
>srini
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
>
You can read in the data using read.delim() or read.table(). For illustration let us generate some artificial data and suppose that you are interested in equal sized breaks of 5 (you can define your own break points instead). x <- rchisq(500000, df=10, ncp=5) brk <- seq(0, 5*ceiling(max(x)/5), by=5) # increments of size 5 h <- hist(x, breaks=brk, plot=FALSE) h$breaks, h$counts will give you the count and break points but I always have trouble matching which interval the counts belong to. Another easier way is to use cut() followed by table() where the labels of cut is helpful. table( cut( x, breaks=brk ) ) As a bonus, you can simplify specifying the break points by including Infinite as the endpoint in cut. brk2 <- seq(0, max(x), by=5) # increments of size 5 table( cut( x, breaks=c(brk2, Inf) ) ) Regards, Adai On Mon, 2005-02-21 at 18:44 -0500, Sean Davis wrote:> Srini > > You should probably look at ?hist. If you look at the "value" section, you > will see that you can get the information you want from the values returned > from hist. If these are microarray probes and intensities, there may be > specific methods for visualizing the data available from the bioconductor > project (www.bioconductor.org). > > Hope this helps, > Sean > > ----- Original Message ----- > From: "Srinivas Iyyer" <srini_iyyer_bio at yahoo.com> > To: "Rhelp" <r-help at stat.math.ethz.ch> > Sent: Monday, February 21, 2005 6:21 PM > Subject: [R] Distribution > > > > Dear group, > > apologies for asking a simple question. I have a file > > where the data looks like this: > > Probe Intensity > > 0:0 501.0 > > 1:0 17760.5 > > 2:0 511.0 > > 3:0 18468.3 > > 4:0 199.8 > > 5:0 508.0 > > 6:0 17241.8 > > 7:0 507.5 > > 8:0 17910.0 > > 9:0 482.5 > > 10:0 17480.3 > > 11:0 434.0 > > 12:0 17631.3 > > 13:0 444.8 > > 14:0 17423.0 > > 15:0 505.3 > > 16:0 16693.0 > > 17:0 438.5 > > 18:0 16920.0 > > 19:0 491.3 > > 20:0 16878.0 > > 21:0 486.3 > > 22:0 16582.0 > > 23:0 483.8 > > 24:0 16694.8 > > 25:0 452.3 > > 26:0 16221.5 > > 27:0 438.3 > > 28:0 17119.8 > > 29:0 455.5 > > 30:0 16579.0 > > 31:0 424.5 > > 32:0 16691.3 > > 33:0 472.0 > > > > > > My question is how do I know the distribution of the > > intensities. My aim is to find out the number of > > intensities or probes that fall in a certain range. > > > > For example 500 probes has intensities ranging from 50 > > to 150. > > > > 300 probes has intensities ranging from 151-250 > > > > I have no clue how to do it for 500,000 probes. Can > > any one please help doing it in R. > > > > thanks and apologies again > > > > srini > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! > > http://www.R-project.org/posting-guide.html > > > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >