On 23/10/2019 7:04 p.m., Ana Marija wrote:
I also tried left_join but I got: Error: std::bad_alloc
df3 <- left_join(l4, asign, by = c("chr","pos")
Error: std::bad_alloc
Looks like bugs in whatever package you're finding "left_join" in (and
previously "merge"). Are those from dplyr and base? Showing us
str(lr), str(asign), and sessionInfo() would be helpful.
Duncan Murdoch
dim(l4)
[1] 166941635 8
dim(asign)
[1] 107371528 5
On Wed, Oct 23, 2019 at 5:32 PM Ana Marija <sokovic.anamar...@gmail.com> wrote:
Hello,
I have two data frames like this:
head(l4)
X1 X2 X3 X4 X5 variant_id pval_nominal gene_id.LCL
1 chr1 13550 G A b38 1:13550:G:A 0.375614 ENSG00000227232
2 chr1 14671 G C b38 1:14671:G:C 0.474708 ENSG00000227232
3 chr1 14677 G A b38 1:14677:G:A 0.699887 ENSG00000227232
4 chr1 16841 G T b38 1:16841:G:T 0.127895 ENSG00000227232
5 chr1 16856 A G b38 1:16856:A:G 0.627822 ENSG00000227232
6 chr1 17005 A G b38 1:17005:A:G 0.802803 ENSG00000227232
head(asign)
gene chr chr_pos pos p.val.Retina
1: ENSG00000227232 chr1 1:10177:A:AC 10177 0.381708
2: ENSG00000227232 chr1 rs145072688:10352:T:TA 10352 0.959523
3: ENSG00000227232 chr1 1:11008:C:G 11008 0.218132
4: ENSG00000227232 chr1 1:11012:C:G 11012 0.218132
5: ENSG00000227232 chr1 1:13110:G:A 13110 0.998262
6: ENSG00000227232 chr1 rs201725126:13116:T:G 13116 0.438572
m = merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
Error in merge.data.frame(l4, asign, by.x = c("X1", "X2"), by.y = c("chr", :
negative length vectors are not allowed
sapply(l4,class)
X1 X2 X3 X4 X5 variant_id
"character" "character" "character" "character" "character" "character"
pval_nominal gene_id.LCL
"numeric" "character"
sapply(asign,class)
gene chr chr_pos pos p.val.Retina
"character" "character" "character" "character" "character"
Please advise as to why I am getting this error when merging?
Thanks
Ana
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