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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]]

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

Hello, All, How can I maintain the decimal places when using write.table()? Jim e.g. df: EFFECT2 PVALUE 1 0.023 0.88080 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: EFFECT2 PVALUE 0.023 0.8808 -0.26 0.08641 -0.114 0.452 [[alternative HTML version deleted]]

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]]

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]]

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

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

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 ALLELES FREQ1 RSQR EFFECT2 STDERR CHISQ PVALUE rs6599753 C,T

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,