[R] negative vector length when merging data frames

[Duncan Murdoch]

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.anamarija using 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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