Hi, This: sum(data[,1]=="GG") may not work because you have some NA in your data. Try this:
sum( data[ , 1 ] == "GG", na.rm = TRUE ) Regards 2009/3/30 David A.G <dasol...@hotmail.com> > > Dear list, > > I am trying to evaluate how many elements in a vector equal a certain > value. The vectors are the columns of a data.frame, read in using > read.table(): > > > dim(data) > [1] 2600 742 > > data[1:5,1:5] > SNP001 SNP002 SNP003 SNP004 SNP005 > 1 GG AA TT TT GG > 2 GG AA TC TT GG > 3 GG AC CC TT GG > 4 AG AA TT TT GG > 5 GG AA TC TT GG > > > table(data[,1]) > > AA AG GG > 251 1093 1252 > > but if I do > > > sum(data[,1]=="GG") > [1] NA > > I have tried storing the column it in a vector but with same results: > > > yyy<-(data[,1]) > > sum(yyy=="GG") > [1] NA > > while if I just get a small number of elements from this vector, it works > fine > > yyyy <- yyy[1:10] > > yyyy > [1] "GG" "GG" "GG" "AG" "GG" "GG" "AA" "GG" "AG" "GG" > > table(yyyy) > yyyy > AA AG GG > 1 2 7 > > sum(yyyy=="GG") > [1] 7 > > I checked the archives for help but couldn´t find my error > What am I missing? > > > sessionInfo() > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > Thanks > > Dave > > > _________________________________________________________________ > > > [[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. > > [[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.
