Hi David
Here it is. You can ignore the bio jargon if it sounds confusing. The
corresponding data type of column (SNP, chr) on which I am applying merge is
same.
merge(data_lane6_snps, data_lane6_snps_rsid , by = c("SNP,"chr"))
str(data_lane6_snps)
'data.frame': 7724462 obs. of 10 variables:
$ chr : Factor w/ 25 levels "chr1","chr10",..: 1 1 1 1 1 1 1 1 1
1 ...
$ SNP : int 100 101 103 108 179 180 191 197 218 222 ...
$ reference : Factor w/ 5 levels "A","C","G","N",..: 2 2 5 2 2 5 2 2 1
5 ...
$ genotype : Factor w/ 10 levels "A","C","G","K",..: 1 1 1 8 2 2 3 8 2
2 ...
$ consensus_qual: int 0 0 0 4 33 33 19 19 19 19 ...
$ snp_qual : int 0 0 0 4 0 33 19 19 19 19 ...
$ rms_qual : int 0 0 0 0 21 21 21 21 21 21 ...
$ depth : int 1 1 1 1 2 2 2 2 2 2 ...
$ bases : Factor w/ 453774 levels "^!,","^!,^!,",..: 5 5 5 410998
49793 155731 284998 416878 133393 133393 ...
$ base_quality : Factor w/ 555104 levels "`","``","```",..: 359 359 359
54813 92856 92856 92856 92856 92539 55424 ...
> str(data_lane6_snps_rsid)
'data.frame': 797807 obs. of 4 variables:
$ chr : Factor w/ 24 levels "1","10","11",..: 3 3 3 3 3 3 3 3 3 3 ...
$ SNP : int 68143872 11071026 69423434 12394791 1302846 95330693 3921381
57122299 41899656 76990037 ...
$ end : int 68143872 11071026 69423434 12394791 1302846 95330693 3921381
57122299 41899656 76990037 ...
$ rsid: Factor w/ 797807 levels "rs10","rs10000010",..: 100229 685690
505395 470219 780326 29342 29263 327909 434159 723152 ...
On Tue, Apr 6, 2010 at 3:59 PM, David Winsemius <[email protected]>wrote:
>
> On Apr 6, 2010, at 3:54 PM, Abhishek Pratap wrote:
>
> Hi Guys
>>
>> I have two data frames which I would like to merge on two conditions.
>>
>> I am doing the following (abstract form)
>>
>> new.data.frame <- merge(df1,df2, by=c("Col1","Col2"))
>>
>
> What does
>
> str(df1) ; str(df2)
>
> ... show?
>
>
>
>> It is giving me a null result.
>>
>> Basically I need to apply two conditions.
>>
>> I also tried sqldf but it is running forever. Will indexing help ?
>>
>> temp <- sqldf("select a.chr,a.SNP,a.snp_qual,a.rms_qual,a.depth,b.rsid
>> FROM
>> + data_lane6_snps a,
>> + data_lane6_snps_rsid b
>> + WHERE
>> + a.SNP = b.SNP
>> + AND
>> + a.chr = b.chr
>> + ")
>>
>> Thanks!
>> -Abhi
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [email protected] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> David Winsemius, MD
> West Hartford, CT
>
>
[[alternative HTML version deleted]]
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