[R] combine all data frame columns into a vector.
Dear All, Could anyone suggest a quick way to combine all columns in a data frame into a vector? For example, I have a data frame of 205 columns with character data types, many data values are repeated in all the columns. Actually, I would like to retrieve all the unique values from this data set. My strategy is to put all column value into a vector and then select unique from that vector. I would appreciate a more efficient method. Thanks. -Sohail The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other priv! ilege. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] combine all data frame columns into a vector.
Thanks Bert, All are character values. -Sohail -Original Message- From: Bert Gunter [mailto:gunter.ber...@gene.com] Sent: Monday, August 12, 2013 4:35 PM To: Khan, Sohail Cc: greatest.possible.newbie; r-help@r-project.org Subject: Re: [R] combine all data frame columns into a vector. Sohail: 1. Are they character or factor? 2. ?unlist unique(unlist(yourframe)) -- Bert On Mon, Aug 12, 2013 at 1:23 PM, Khan, Sohail skha...@nshs.edu wrote: Dear All, Could anyone suggest a quick way to combine all columns in a data frame into a vector? For example, I have a data frame of 205 columns with character data types, many data values are repeated in all the columns. Actually, I would like to retrieve all the unique values from this data set. My strategy is to put all column value into a vector and then select unique from that vector. I would appreciate a more efficient method. Thanks. -Sohail The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other pr! iv! ilege. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other priv! ilege. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] combine all data frame columns into a vector.
Thanks Arun and Bert. Both options work. -Sohail -Original Message- From: arun [mailto:smartpink...@yahoo.com] Sent: Monday, August 12, 2013 4:51 PM To: Khan, Sohail Cc: R help Subject: Re: [R] combine all data frame columns into a vector. Hi, May be this help: dat1- structure(list(V1 = c(h, f, s, n, r, x, h, t, u, g), V2 = c(p, j, r, r, i, x, f, b, n, d), V3 = c(c, o, s, d, f, r, b, p, q, b ), V4 = c(i, g, j, d, y, f, s, q, s, z), V5 = c(m, j, h, f, b, b, k, j, g, i), V6 = c(m, w, m, s, o, z, l, h, e, d), V7 = c(m, g, h, d, s, i, y, z, t, m), V8 = c(d, f, a, z, q, i, o, v, a, s), V9 = c(n, d, n, f, j, j, g, w, k, v), V10 = c(i, t, y, c, m, p, q, c, k, m)), .Names = c(V1, V2, V3, V4, V5, V6, V7, V8, V9, V10), row.names = c(NA, -10L), class = data.frame) unique(unlist(dat1)) # [1] h f s n r x t u g p j i b d c o q y z #[20] m k w l e a v #or unique(as.vector(as.matrix(dat1))) # [1] h f s n r x t u g p j i b d c o q y z #[20] m k w l e a v A.K. - Original Message - From: Khan, Sohail skha...@nshs.edu To: 'greatest.possible.newbie' daniel.h...@gmx.net; r-help@r-project.org r-help@r-project.org Cc: Sent: Monday, August 12, 2013 4:23 PM Subject: [R] combine all data frame columns into a vector. Dear All, Could anyone suggest a quick way to combine all columns in a data frame into a vector? For example, I have a data frame of 205 columns with character data types, many data values are repeated in all the columns. Actually, I would like to retrieve all the unique values from this data set. My strategy is to put all column value into a vector and then select unique from that vector. I would appreciate a more efficient method. Thanks. -Sohail The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other priv! ilege. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to transpose it in a fast way?
Perhaps you could process this with a unix/Linux utility Awk, before reading
the file into R.
-Sohail
From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of
peter dalgaard [pda...@gmail.com]
Sent: Friday, March 08, 2013 5:08 AM
To: Yao He
Cc: R help
Subject: Re: [R] How to transpose it in a fast way?
On Mar 7, 2013, at 01:18 , Yao He wrote:
Dear all:
I have a big data file of 6 columns and 6 rows like that:
AA AC AA AA ...AT
CC CC CT CT...TC
..
.
I want to transpose it and the output is a new like that
AA CC
AC CC
AA CT.
AA CT.
AT TC.
The keypoint is I can't read it into R by read.table() because the
data is too large,so I try that:
c-file(silygenotype.txt,r)
geno_t-list()
repeat{
line-readLines(c,n=1)
if (length(line)==0)break #end of file
line-unlist(strsplit(line,\t))
geno_t-cbind(geno_t,line)
}
write.table(geno_t,xxx.txt)
It works but it is too slow ,how to optimize it???
As others have pointed out, that's a lot of data!
You seem to have the right idea: If you read the columns line by line there is
nothing to transpose. A couple of points, though:
- The cbind() is a potential performance hit since it copies the list every
time around. geno_t - vector(list, 6) and then
geno_t[[i]] - etc
- You might use scan() instead of readLines, strsplit
- Perhaps consider the data type as you seem to be reading strings with 16
possible values (I suspect that R already optimizes string storage to make this
point moot, though.)
--
Peter Dalgaard, Professor
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
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[R] Calculateing means
Dear List, I have a data matrix with 570 columns containing 95 (samples) with 6 replicates each. How can I calculate the mean of the replicates for 95 samples? Thank you. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other priv! ilege. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calculateing means
Thanks. But aggregate will work on rows or columns. I need to calculate mean for subsets of rows in a matrix I.E. Indx x1 x2 x3 x4 x5 x6 x7 x8 x9 1 25 30 15 8 12 9 18 21 89 2 52 35 42 74 65 20 28 32 12 3 12 35 33 88 12 52 32 32 18 4 25 25 16 23 89 21 21 21 42 ... I would like to calculate means for x1-x3, x4-x6, x7-x9 For each row. -Sohail -Original Message- From: John Kane [mailto:jrkrid...@inbox.com] Sent: Friday, November 16, 2012 4:35 PM To: Khan, Sohail; 'r-help@r-project.org' Subject: RE: [R] Calculateing means ?aggregate will do it. x - data.frame( height= c(50, 174, 145, 200, 210, 140, 175), age_group=c(1,2,2,1,1,2,1), ville= c(1,2,3,1,2,3,1)) aggregate(x$height,list(x$age_group, x$ville), mean) or have a look at the plyr or datatable packages. John Kane Kingston ON Canada -Original Message- From: skha...@nshs.edu Sent: Fri, 16 Nov 2012 15:58:17 -0500 To: r-help@r-project.org Subject: [R] Calculateing means Dear List, I have a data matrix with 570 columns containing 95 (samples) with 6 replicates each. How can I calculate the mean of the replicates for 95 samples? Thank you. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other priv! ilege. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Send any screenshot to your friends in seconds... Works in all emails, instant messengers, blogs, forums and social networks. TRY IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if2 for FREE The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other priv! ilege. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
