Hi, How about this:
> SNP5 <- merge(SNP4, SNP1[,2:3], all.x=TRUE) > SNP5 Marker Animal Y x 1 P1001 194073197 0.021088 2 2 P1002 194073197 0.021088 1 3 P1004 194073197 0.021088 2 4 P1005 194073197 0.021088 0 5 P1006 194073197 0.021088 2 6 P1007 194073197 0.021088 0 This ignores Animal, and that may or may not be what you want - it wasn't clear from your question. But your error is due to memory limitations - could be due to specifying the wrong merge, or to having files larger than your computer can handle. This is a good job for a proper database. >> SNP5 <- merge(SNP4, SNP1$x, by.x = 'Marker', by.y = 'Marker', all = TRUE) > Error in fix.by(by.y, y) : 'by' must specify valid column(s) If you just include SNP1$x, there is no Marker column to merge on. You need to include at least two columns. On Wed, Apr 22, 2009 at 3:30 AM, joe1985 <johan...@dsr.life.ku.dk> wrote: > > Hello > > I have two data frames, SNP4 and SNP1: > >> head(SNP4) > Animal Marker Y > 3213 194073197 P1001 0.021088 > 1295 194073197 P1002 0.021088 > 915 194073197 P1004 0.021088 > 2833 194073197 P1005 0.021088 > 1487 194073197 P1006 0.021088 > 1885 194073197 P1007 0.021088 > >> head(SNP1) > Animal Marker x > 3213 194073197 P1001 2 > 1295 194073197 P1002 1 > 915 194073197 P1004 2 > 2833 194073197 P1005 0 > 1487 194073197 P1006 2 > 1885 194073197 P1007 0 > > I want these two data frames merged by 'Marker', but when i try > >> SNP5 <- merge(SNP4, SNP1, by = 'Marker', all = TRUE) > Error: cannot allocate vector of size 2.4 Gb > In addition: Warning messages: > 1: In merge.data.frame(SNP4, SNP1, by = "Marker", all = TRUE) : > Reached total allocation of 1535Mb: see help(memory.size) > 2: In merge.data.frame(SNP4, SNP1, by = "Marker", all = TRUE) : > Reached total allocation of 1535Mb: see help(memory.size) > 3: In merge.data.frame(SNP4, SNP1, by = "Marker", all = TRUE) : > Reached total allocation of 1535Mb: see help(memory.size) > 4: In merge.data.frame(SNP4, SNP1, by = "Marker", all = TRUE) : > Reached total allocation of 1535Mb: see help(memory.size) > > And error occurs. > > What i want is the column SNP1$x merged together with SNP4 by Marker, so > some markers will have NA's in the 'x'-column in the SNP5 dataset. > > I also tried this > >> SNP5 <- merge(SNP4, SNP1$x, by.x = 'Marker', by.y = 'Marker', all = TRUE) > Error in fix.by(by.y, y) : 'by' must specify valid column(s) > > I won't work either. > > Does anyone have any idea how to solve this. > > Regards, > > Johannes. > > > > -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ 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.
