[R] Merging data frames, or one column/vector with a data frame filling out empty rows with NA's

joe1985 johannes at dsr.life.ku.dk
Wed Apr 22 09:30:02 CEST 2009


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.




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