Re: [R] sort by column and row names
Yes, that is it. Thank you very much, Phil. -Original Message- From: Phil Spector [mailto:spec...@stat.berkeley.edu] Sent: Thursday, February 17, 2011 3:36 PM To: Jim Moon Cc: r-help@r-project.org Subject: Re: [R] sort by column and row names Jim - I believe dat[order(rownames(dat)),order(colnames(dat))] is what you are looking for. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Thu, 17 Feb 2011, Jim Moon wrote: > Hello, All, > > How can one sort on column and row names. For example: > > How can this > X1 X3 X2 > X1 1 0 0 > X3 0 1 0 > X2 0 0 1 > > become this? > X1 X2 X3 > X1 1 0 0 > X2 0 1 0 > X3 0 0 1 > > > Thank you for your time! > > Jim > > > [[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. > __ 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.
[R] sort by column and row names
Hello, All, How can one sort on column and row names. For example: How can this X1 X3 X2 X1 1 0 0 X3 0 1 0 X2 0 0 1 become this? X1 X2 X3 X1 1 0 0 X2 0 1 0 X3 0 0 1 Thank you for your time! Jim [[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.
[R] GWAF package: lme.batch.imputed(): object 'kmat' not found
Hello, All,
GWAF 1.2
R.Version() is below.
system(lme.batch.imputed(
phenfile = 'phenfile.csv',
genfile = 'CARe_imputed_release.0.fhsR.gz',
pedfile='pedfile.csv',
phen='phen1',
covar=c('covar1','covar2'),
kinmat='imputed_fhs.kinship.RData',
outfile='imputed.FHS.IBC.GWAF.LME.output.0.txt'
))
Gives the error messages:
Error in coxme.varcheck(ncluster, varlist, n, gvars, groups, sparse, rescale, :
object 'kmat' not found
Error in lme.cov.out$theta : $ operator is invalid for atomic vectors
Might anyone know why?
Thank you for your time!
Jim
---
> R.Version()
$platform
[1] "x86_64-apple-darwin9.6.0"
$arch
[1] "x86_64"
$os
[1] "darwin9.6.0"
$system
[1] "x86_64, darwin9.6.0"
$status
[1] ""
$major
[1] "2"
$minor
[1] "12.1"
$year
[1] "2010"
$month
[1] "12"
$day
[1] "16"
$`svn rev`
[1] "53855"
$language
[1] "R"
$version.string
[1] "R version 2.12.1 (2010-12-16)"
[[alternative HTML version deleted]]
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Re: [R] write.table -- maintain decimal places
Great. Thank you, Peter!
-Original Message-
From: Peter Ehlers [mailto:ehl...@ucalgary.ca]
Sent: Tuesday, January 25, 2011 7:26 PM
To: Jim Moon
Cc: r-help@r-project.org
Subject: Re: [R] write.table -- maintain decimal places
On 2011-01-25 17:22, Jim Moon wrote:
> Thank you for the response, Peter.
>
> The approach:
> write.table(format(df,
> drop0trailing=FALSE),file='df.txt',quote=F,sep='\t',row.names=F)
> surprisingly still results in some loss of trailing 0's.
Here are a couple more (essentially identical) ways:
# 1.
dfm <- within(df, {
EFFECT2 <- sprintf("%6.3f", EFFECT2)
PVALUE <- sprintf("%7.5f", PVALUE)
})
# 2.
dfm <- within(df, {
EFFECT2 <- formatC(EFFECT2, format="f", digits=3)
PVALUE <- formatC(PVALUE, format="f", digits=5)
})
write.table(dfm, file='dfm.txt', quote=FALSE, sep='\t', row.names=FALSE)
Peter Ehlers
>
> df:
> EFFECT2 PVALUE
> 1 0.0230.88080
> 2 -0.260 0.08641
> 3 -0.114 0.45200
>
> df.txt:
> EFFECT2PVALUE
> 0.023 8.808e-01
> -0.26 8.641e-02
> -0.114 4.520e-01
>
>
> -Original Message-
> From: Peter Ehlers [mailto:ehl...@ucalgary.ca]
> Sent: Tuesday, January 25, 2011 5:09 PM
> To: Jim Moon
> Cc: r-help@r-project.org
> Subject: Re: [R] write.table -- maintain decimal places
>
> On 2011-01-25 16:16, Jim Moon wrote:
>> Hello, All,
>>
>> How can I maintain the decimal places when using write.table()?
>>
>> Jim
>>
>> e.g.
>>
>> df:
>> EFFECT2 PVALUE
>> 1 0.0230.88080
>> 2 -0.260 0.08641
>> 3 -0.114 0.45200
>>
>> write.table(df,file='df.txt',quote=F,sep='\t',row.names=F)
>
>write.table(format(df, drop0trailing=FALSE), )
>
> Peter Ehlers
>
>>
>>
>> df.txt:
>> EFFECT2PVALUE
>> 0.023 0.8808
>> -0.26 0.08641
>> -0.114 0.452
>>
>> [[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.
>
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] write.table -- maintain decimal places
I am using: "R version 2.11.1 (2010-05-31)" It is good to know that it works in 2.12.1 Jim -Original Message- From: Peter Ehlers [mailto:ehl...@ucalgary.ca] Sent: Tuesday, January 25, 2011 5:57 PM To: Jim Moon Cc: r-help@r-project.org Subject: Re: [R] write.table -- maintain decimal places On 2011-01-25 17:22, Jim Moon wrote: > Thank you for the response, Peter. > > The approach: > write.table(format(df, > drop0trailing=FALSE),file='df.txt',quote=F,sep='\t',row.names=F) > surprisingly still results in some loss of trailing 0's. > What version of R? I'm using R version 2.12.1 Patched (2010-12-27 r53883) and it works for me. Peter Ehlers > df: > EFFECT2 PVALUE > 1 0.0230.88080 > 2 -0.260 0.08641 > 3 -0.114 0.45200 > > df.txt: > EFFECT2PVALUE > 0.023 8.808e-01 > -0.26 8.641e-02 > -0.114 4.520e-01 > > > -Original Message----- > From: Peter Ehlers [mailto:ehl...@ucalgary.ca] > Sent: Tuesday, January 25, 2011 5:09 PM > To: Jim Moon > Cc: r-help@r-project.org > Subject: Re: [R] write.table -- maintain decimal places > > On 2011-01-25 16:16, Jim Moon wrote: >> Hello, All, >> >> How can I maintain the decimal places when using write.table()? >> >> Jim >> >> e.g. >> >> df: >> EFFECT2 PVALUE >> 1 0.0230.88080 >> 2 -0.260 0.08641 >> 3 -0.114 0.45200 >> >> write.table(df,file='df.txt',quote=F,sep='\t',row.names=F) > >write.table(format(df, drop0trailing=FALSE), ) > > Peter Ehlers > >> >> >> df.txt: >> EFFECT2PVALUE >> 0.023 0.8808 >> -0.26 0.08641 >> -0.114 0.452 >> >> [[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. > __ 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] write.table -- maintain decimal places
Thank you for the response, Peter. The approach: write.table(format(df, drop0trailing=FALSE),file='df.txt',quote=F,sep='\t',row.names=F) surprisingly still results in some loss of trailing 0's. df: EFFECT2 PVALUE 1 0.0230.88080 2 -0.260 0.08641 3 -0.114 0.45200 df.txt: EFFECT2PVALUE 0.023 8.808e-01 -0.26 8.641e-02 -0.114 4.520e-01 -Original Message- From: Peter Ehlers [mailto:ehl...@ucalgary.ca] Sent: Tuesday, January 25, 2011 5:09 PM To: Jim Moon Cc: r-help@r-project.org Subject: Re: [R] write.table -- maintain decimal places On 2011-01-25 16:16, Jim Moon wrote: > Hello, All, > > How can I maintain the decimal places when using write.table()? > > Jim > > e.g. > > df: >EFFECT2 PVALUE > 1 0.0230.88080 > 2 -0.260 0.08641 > 3 -0.114 0.45200 > > write.table(df,file='df.txt',quote=F,sep='\t',row.names=F) write.table(format(df, drop0trailing=FALSE), ) Peter Ehlers > > > df.txt: > EFFECT2PVALUE > 0.023 0.8808 > -0.26 0.08641 > -0.114 0.452 > > [[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. __ 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.
[R] write.table -- maintain decimal places
Hello, All, How can I maintain the decimal places when using write.table()? Jim e.g. df: EFFECT2 PVALUE 1 0.0230.88080 2 -0.260 0.08641 3 -0.114 0.45200 write.table(df,file='df.txt',quote=F,sep='\t',row.names=F) df.txt: EFFECT2PVALUE 0.023 0.8808 -0.26 0.08641 -0.114 0.452 [[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] read in data, maintain decimal places
David, Perfect. Thank you! Jim -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Friday, January 14, 2011 2:26 PM To: Jim Moon Cc: r-help@r-project.org Subject: Re: [R] read in data, maintain decimal places On Jan 14, 2011, at 5:22 PM, Jim Moon wrote: > Good day, All, > > Is there any way to maintain the number of decimal places in the > type of situation below? > I would like to maintain the number of decimal places in 0.667, > despite the fact that its column-mates have a fourth decimal place. You would need to read it as character. If that is your choice then use the colClasses argument. > > Thank you for your time. > > Jim > > dat.txt contents: > > MARKER ALLELESFREQ1 RSQR EFFECT2STDERR > CHISQ PVALUE > rs6599753 C,T .2087 .1866 0.166 0.387 > 0.1850 0.6671 > rs12443141 A,T .2087 .1868 0.166 0.386 > 0.1851 0.667 > rs12905389 A,G .2806 .6149 -0.038 0.193 > 0.0381 0.8452 > > R: >> dat = read.delim( dat.txt) >> dat > MARKER ALLELES FREQ1 RSQR EFFECT2 STDERR CHISQ PVALUE > 1 rs6599753 C,T 0.2087 0.1866 0.166 0.387 0.1850 0.6671 > 2 rs12443141 A,T 0.2087 0.1868 0.166 0.386 0.1851 0.6670 > 3 rs12905389 A,G 0.2806 0.6149 -0.038 0.193 0.0381 0.8452 > -- David Winsemius, MD West Hartford, CT __ 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.
[R] read in data, maintain decimal places
Good day, All, Is there any way to maintain the number of decimal places in the type of situation below? I would like to maintain the number of decimal places in 0.667, despite the fact that its column-mates have a fourth decimal place. Thank you for your time. Jim dat.txt contents: MARKER ALLELESFREQ1 RSQR EFFECT2STDERR CHISQ PVALUE rs6599753 C,T .2087 .1866 0.166 0.387 0.1850 0.6671 rs12443141 A,T .2087 .1868 0.166 0.386 0.1851 0.667 rs12905389 A,G .2806 .6149 -0.038 0.193 0.0381 0.8452 R: >dat = read.delim( dat.txt) >dat MARKER ALLELES FREQ1 RSQR EFFECT2 STDERR CHISQ PVALUE 1 rs6599753 C,T 0.2087 0.1866 0.166 0.387 0.1850 0.6671 2 rs12443141 A,T 0.2087 0.1868 0.166 0.386 0.1851 0.6670 3 rs12905389 A,G 0.2806 0.6149 -0.038 0.193 0.0381 0.8452 [[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.
[R] with(data.frame,ifelse(___,___,___))
Hello, All, Mac OS 10.6.5 R64 2.11.1 This works as expected: f1 = c(0.084, 0.099, 0) data= data.frame(f1) data$f1=with(data,ifelse(f1==0, 0.0001, f1)) data f1 1 0.0840 2 0.0990 3 0.0001 Substituting 'f1==0' with 'T' produces the expected result: f1 = c(0.084, 0.099, 0) data= data.frame(f1) data$f1=with(data,ifelse(T, 0.0001, f1)) data f1 1 1e-04 2 1e-04 3 1e-04 But, substituting 'f1==0' or 'T' with 'F' does not produce the expected result: f1 = c(0.084, 0.099, 0) data= data.frame(f1) data$f1=with(data,ifelse(F, 0.0001, f1)) data f1 1 0.084 2 0.084 3 0.084 I would expect this: f1 1 0.084 2 0.099 3 0 Is with(data.frame,ifelse(___,___,___)) broken, or does my interpretation of it need fixing? Thank you for your time. Jim [[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.
[R] Write.table eol argument
Hello All, R 2.11.1 Windows XP, 32-bit Help says that default is eol='\n'. To me, that represents Linefeed (LF) >From Help: eol the character(s) to print at the end of each line (row). For example, eol="\r\n" will produce Windows' line endings on a Unix-alike OS, and eol="\r" will produce files as expected by Mac OS Excel 2004. I would like for write.table to end each line with LF only-no carriage return (CR). Default eol='\n' generates CRLF Explicit eol='\n' generates CRLF eol='\r' generates CR eol='\r\n' generates (predictably) CRCRLF Thank you for your time. Jim [[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] sd() for numeric row entries
This is very helpful, Phil. Being new to R and trying to get a handle on *apply, by, aggregate... this is great. Thank you. Jim -Original Message- From: Phil Spector [mailto:spec...@stat.berkeley.edu] Sent: Wednesday, December 08, 2010 2:36 PM To: Jim Moon Cc: r-help@r-project.org Subject: Re: [R] sd() for numeric row entries Jim - Suppose the data frame is named "df". Then df$std_dev = apply(df,1,sd,na.rm=TRUE) will do what you want, although it will generate some warning messages due to the first column. df$sd_dev = apply(df[,sapply(df,is.numeric)],1,sd) does the same, but won't produce warnings. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Wed, 8 Dec 2010, Jim Moon wrote: > How might one calculate standard deviation, row-wise, for the numeric values > in a data frame such as this one > V1 V2 V3 V4 V5 > 1 rs11089130 0.4565 0.4574 0.4569 0.4572 > 2 rs738829 0.6548 0.6519 0.6448 0.6549 > 3 rs915674 0.7503 0.7500 0.7517 0.7502 > > and place the standard deviation in a 6th column called ???std_dev > > Regards, > Jim > > > [[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.
[R] sd() for numeric row entries
How might one calculate standard deviation, row-wise, for the numeric values in a data frame such as this one V1 V2 V3 V4 V5 1 rs11089130 0.4565 0.4574 0.4569 0.4572 2 rs738829 0.6548 0.6519 0.6448 0.6549 3 rs915674 0.7503 0.7500 0.7517 0.7502 and place the standard deviation in a 6th column called âstd_devâ? Regards, Jim [[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] FW: how to use by() ?
Well-phrased, David. :-)
Jim
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Monday, November 29, 2010 10:53 AM
To: Jim Moon
Cc: r-help@r-project.org
Subject: Re: [R] FW: how to use by() ?
On Nov 29, 2010, at 1:36 PM, Jim Moon wrote:
> Thank you for the suggestion, Bill. The result is not quite what I
> would like. Here's sample code for you or anyone else who may be
> interested:
>
> Al1 = c('A','C','C','C')
> Al2 = c('G','G','G','T')
> Freq1 = c(0.0078,0.0567,0.9434,0.9908)
> MAF = c(0.0078,0.0567,0.0566,0.0092)
> m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='')
> m1
>
> Al1 Al2 Freq1MAF major_allele
> 1 A G 0.0078 0.0078
> 2 C G 0.0567 0.0567
> 3 C G 0.9434 0.0566
> 4 C T 0.9908 0.0092
>
>
> Using the suggestion involving "with()" (I swapped Al1 and Al2 from
> before, but this does not affect the nature of the output):
>
> m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al2, Al1));m1
>
> Al1 Al2 Freq1MAF major_allele
I suspect that you have just been bitten by the data.frame-
stringsAsFactors=TRUE crocodile. Since you are comparing floating
point numbers, you are also wading in rivers where floating-point
crocodiles are also hungry and searching out their next victim.
--
David.
> 1 A G 0.0078 0.00781
> 2 C G 0.0567 0.05671
> 3 C G 0.9434 0.05662
> 4 C T 0.9908 0.00922
>
>
> The output I desire is:
> Al1 Al2 Freq1MAF major_allele
> 1 A G 0.0078 0.0078G
> 2 C G 0.0567 0.0567G
> 3 C G 0.9434 0.0566C
> 4 C T 0.9908 0.0092C
>
>
> Jim
>
>
> -Original Message-
> From: William Dunlap [mailto:wdun...@tibco.com]
> Sent: Monday, November 29, 2010 10:02 AM
> To: Jim Moon
> Subject: RE: [R] how to use by() ?
>
> m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al1, Al2))
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
>> -Original Message-
>> From: r-help-boun...@r-project.org
>> [mailto:r-help-boun...@r-project.org] On Behalf Of Jim Moon
>> Sent: Monday, November 29, 2010 9:44 AM
>> To: r-help@r-project.org
>> Subject: [R] how to use by() ?
>>
>> Hello, All!
>>
>> How might one accomplish this using the by() function?
>> m1 is a data frame.
>>
>> # populate column "m1$major_allele"
>> for ( i in 1:length(m1$major_allele)) {
>> if ( m1$Freq1[i] == m1$MAF[i]){
>>m1$major_allele[i] = m1$Al1[i]
>> }
>> else{
>> m1$major_allele[i] = m1$Al2[i]
>> }
>> }
>>
>>
>> Jim
>>
>> [[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.
>>
>
> __
> 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.
David Winsemius, MD
West Hartford, CT
__
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] FW: how to use by() ?
Thank you, Bill. That fixed it.
Jim
-Original Message-
From: William Dunlap [mailto:wdun...@tibco.com]
Sent: Monday, November 29, 2010 10:46 AM
To: Jim Moon; r-help@r-project.org
Subject: RE: [R] FW: how to use by() ?
ifelse(cond,ifTrue,ifFalse) doesn't do what you
want when ifTrue or ifElse is a factor.
You can use as.character on the factors
> with(m1, ifelse(Freq1==MAF, as.character(Al2), as.character(Al1)))
[1] "G" "G" "C" "C"
or use the stringsAsFactors=FALSE argument to
data.frame (or read.table) when you make the
data.frame.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Jim Moon
> Sent: Monday, November 29, 2010 10:37 AM
> To: r-help@r-project.org
> Subject: [R] FW: how to use by() ?
>
> Thank you for the suggestion, Bill. The result is not quite
> what I would like. Here's sample code for you or anyone else
> who may be interested:
>
> Al1 = c('A','C','C','C')
> Al2 = c('G','G','G','T')
> Freq1 = c(0.0078,0.0567,0.9434,0.9908)
> MAF = c(0.0078,0.0567,0.0566,0.0092)
> m1 = data.frame(Al1=Al1,
> Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='')
> m1
>
> Al1 Al2 Freq1MAF major_allele
> 1 A G 0.0078 0.0078
> 2 C G 0.0567 0.0567
> 3 C G 0.9434 0.0566
> 4 C T 0.9908 0.0092
>
>
> Using the suggestion involving "with()" (I swapped Al1 and
> Al2 from before, but this does not affect the nature of the output):
>
> m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al2, Al1));m1
>
> Al1 Al2 Freq1MAF major_allele
> 1 A G 0.0078 0.00781
> 2 C G 0.0567 0.05671
> 3 C G 0.9434 0.05662
> 4 C T 0.9908 0.00922
>
>
> The output I desire is:
> Al1 Al2 Freq1MAF major_allele
> 1 A G 0.0078 0.0078 G
> 2 C G 0.0567 0.0567G
> 3 C G 0.9434 0.0566C
> 4 C T 0.9908 0.0092C
>
>
> Jim
>
>
> -Original Message-
> From: William Dunlap [mailto:wdun...@tibco.com]
> Sent: Monday, November 29, 2010 10:02 AM
> To: Jim Moon
> Subject: RE: [R] how to use by() ?
>
> m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al1, Al2))
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
> > -Original Message-
> > From: r-help-boun...@r-project.org
> > [mailto:r-help-boun...@r-project.org] On Behalf Of Jim Moon
> > Sent: Monday, November 29, 2010 9:44 AM
> > To: r-help@r-project.org
> > Subject: [R] how to use by() ?
> >
> > Hello, All!
> >
> > How might one accomplish this using the by() function?
> > m1 is a data frame.
> >
> > # populate column "m1$major_allele"
> > for ( i in 1:length(m1$major_allele)) {
> > if ( m1$Freq1[i] == m1$MAF[i]){
> > m1$major_allele[i] = m1$Al1[i]
> > }
> > else{
> > m1$major_allele[i] = m1$Al2[i]
> > }
> > }
> >
> >
> > Jim
> >
> > [[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.
> >
>
> __
> 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.
>
__
R-help@r-project.org mailing list
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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 use by() ?
Jim Moon ohsu.edu> writes:
> How might one accomplish this using the by() function?
> m1 is a data frame.
>
> # populate column "m1$major_allele"
> for ( i in 1:length(m1$major_allele)) {
> if ( m1$Freq1[i] == m1$MAF[i]){
> m1$major_allele[i] = m1$Al1[i]
> }
> else{
> m1$major_allele[i] = m1$Al2[i]
> }
> }
You could use:
m1$major_allele <- ifelse( m1$Freq1 == m1$MAF, m1$Al1, m1$Al2 )
Greg
---
Thank you for the suggestion, Greg. The result is not quite what I would like.
Here's sample code for you or anyone else who may be interested:
Al1 = c('A','C','C','C')
Al2 = c('G','G','G','T')
Freq1 = c(0.0078,0.0567,0.9434,0.9908)
MAF = c(0.0078,0.0567,0.0566,0.0092)
m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='')
m1
Al1 Al2 Freq1MAF major_allele
1 A G 0.0078 0.0078
2 C G 0.0567 0.0567
3 C G 0.9434 0.0566
4 C T 0.9908 0.0092
Using the suggestion involving "ifelse" (I swapped Al1 and Al2 from before, but
this does not affect the nature of the output):
m1$major_allele <- ifelse( m1$Freq1 == m1$MAF, m1$Al2, m1$Al1 );m1
Al1 Al2 Freq1MAF major_allele
1 A G 0.0078 0.00781
2 C G 0.0567 0.05671
3 C G 0.9434 0.05662
4 C T 0.9908 0.00922
The output I desire is:
Al1 Al2 Freq1MAF major_allele
1 A G 0.0078 0.0078G
2 C G 0.0567 0.0567G
3 C G 0.9434 0.0566C
4 C T 0.9908 0.0092C
Jim
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] FW: how to use by() ?
Thank you for the suggestion, Bill. The result is not quite what I would like.
Here's sample code for you or anyone else who may be interested:
Al1 = c('A','C','C','C')
Al2 = c('G','G','G','T')
Freq1 = c(0.0078,0.0567,0.9434,0.9908)
MAF = c(0.0078,0.0567,0.0566,0.0092)
m1 = data.frame(Al1=Al1, Al2=Al2,Freq1=Freq1,MAF=MAF,major_allele='')
m1
Al1 Al2 Freq1MAF major_allele
1 A G 0.0078 0.0078
2 C G 0.0567 0.0567
3 C G 0.9434 0.0566
4 C T 0.9908 0.0092
Using the suggestion involving "with()" (I swapped Al1 and Al2 from before, but
this does not affect the nature of the output):
m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al2, Al1));m1
Al1 Al2 Freq1MAF major_allele
1 A G 0.0078 0.00781
2 C G 0.0567 0.05671
3 C G 0.9434 0.05662
4 C T 0.9908 0.00922
The output I desire is:
Al1 Al2 Freq1MAF major_allele
1 A G 0.0078 0.0078G
2 C G 0.0567 0.0567G
3 C G 0.9434 0.0566C
4 C T 0.9908 0.0092C
Jim
-Original Message-
From: William Dunlap [mailto:wdun...@tibco.com]
Sent: Monday, November 29, 2010 10:02 AM
To: Jim Moon
Subject: RE: [R] how to use by() ?
m1$major_allele <- with(m1, ifelse(Freq1==MAF, Al1, Al2))
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Jim Moon
> Sent: Monday, November 29, 2010 9:44 AM
> To: r-help@r-project.org
> Subject: [R] how to use by() ?
>
> Hello, All!
>
> How might one accomplish this using the by() function?
> m1 is a data frame.
>
> # populate column "m1$major_allele"
> for ( i in 1:length(m1$major_allele)) {
> if ( m1$Freq1[i] == m1$MAF[i]){
> m1$major_allele[i] = m1$Al1[i]
> }
> else{
> m1$major_allele[i] = m1$Al2[i]
> }
> }
>
>
> Jim
>
> [[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.
>
__
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.
[R] how to use by() ?
Hello, All!
How might one accomplish this using the by() function?
m1 is a data frame.
# populate column "m1$major_allele"
for ( i in 1:length(m1$major_allele)) {
if ( m1$Freq1[i] == m1$MAF[i]){
m1$major_allele[i] = m1$Al1[i]
}
else{
m1$major_allele[i] = m1$Al2[i]
}
}
Jim
[[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.
