On Apr 22, 2009, at 5:22 AM, Johannes G. Madsen 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.
So what are the results of:
str(SNP4) ; str(SNP1) # this will tell us how large these objects
are.
And are you sure you don't want the merge to occur by Animal as well?
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.
The second error seems pretty obvious. You are trying to merge a
vector that has no longer any "Marker" with a dataframe that does.
Regards,
Johannes.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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