Dear Ana
Since this appears to be genetics data have you thought of looking at
Bioconductor for help? I do not use genetic data-sets but people there
must use big files every day three times before breakfast.
Michael
On 24/10/2019 00:33, Ana Marija wrote:
thanks but I would need solution in R
On Wed, Oct 23, 2019 at 6:31 PM Jim Lemon <drjimle...@gmail.com> wrote:
I don't have it installed - that was merely a suggestion. I notice
that both data.table and dplyr packages are mentioned as possibilities
for "merge big datasets in r". Apparently the best way to do it if you
have a database manager is to read the two datasets into tables and do
the join via SQL or whatever language is available.
Jim
On Thu, Oct 24, 2019 at 10:17 AM Ana Marija <sokovic.anamar...@gmail.com> wrote:
no can you please send me an example how the command would look like in my case?
On Wed, Oct 23, 2019 at 6:16 PM Jim Lemon <drjimle...@gmail.com> wrote:
Yes. Have you tried the bigmemory package?
Jim
On Thu, Oct 24, 2019 at 10:08 AM Ana Marija <sokovic.anamar...@gmail.com> wrote:
Hi Jim,
I think one of the issue is that data frames are so big,
dim(l4)
[1] 166941635 8
dim(asign)
[1] 107371528 5
so my example would not reproduce the error
On Wed, Oct 23, 2019 at 6:05 PM Jim Lemon <drjimle...@gmail.com> wrote:
Hi Ana,
When I run this example taken from your email:
l4<-read.table(text="X1 X2 X3 X4 X5 variant_id pval_nominal gene_id.LCL
chr1 13550 G A b38 1:13550:G:A 0.375614 ENSG00000227232
chr1 14671 G C b38 1:14671:G:C 0.474708 ENSG00000227232
chr1 14677 G A b38 1:14677:G:A 0.699887 ENSG00000227232
chr1 16841 G T b38 1:16841:G:T 0.127895 ENSG00000227232
chr1 16856 A G b38 1:16856:A:G 0.627822 ENSG00000227232
chr1 17005 A G b38 1:17005:A:G 0.802803 ENSG00000227232",
header=TRUE,stringsAsFactors=FALSE)
asign<-read.table(text="gene chr chr_pos pos p.val.Retina
ENSG00000227232 chr1 1:10177:A:AC 10177 0.381708
ENSG00000227232 chr1 rs145072688:10352:T:TA 10352 0.959523
ENSG00000227232 chr1 1:11008:C:G 11008 0.218132
ENSG00000227232 chr1 1:11012:C:G 11012 0.218132
ENSG00000227232 chr1 1:13110:G:A 13110 0.998262
ENSG00000227232 chr1 rs201725126:13116:T:G 13116 0.438572",
header=TRUE,stringsAsFactors=FALSE)
merge(l4, asign, by.x=c("X1", "X2"), by.y=c("chr", "pos"))
[1] X1 X2 X3 X4 X5
[6] variant_id pval_nominal gene_id.LCL gene chr_pos
[11] p.val.Retina
<0 rows> (or 0-length row.names)
It works okay, but there are no matches in the join. So I can't even
guess what the problem is.
Jim
On Thu, Oct 24, 2019 at 9:33 AM 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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______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Michael
http://www.dewey.myzen.co.uk/home.html
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
