Just so you know
length(intersect(data_lane6_snps$SNP, data_lane6_snps_rsid$SNP))
796120
I just need to include the chr condition now where I am stuck.
-Abhi
On Tue, Apr 6, 2010 at 4:51 PM, Abhishek Pratap <abhishek....@gmail.com>wrote:
> Hi David
>
> I can understand looking the SNP data values it can be felt that they are
> different values and hence no result in merge. However the columns still
> have ~700K SNPs common. What I am looking for is a merge where the SNP and
> Chr matches. If I match only the SNP column I get partially correct results
> since it is possible for two chromosomes to have a SNP at the same bp
> location so the merge needs to take both SNP position and Chromosome into
> account.
>
> Thanks!
> -Abhi
>
>
> On Tue, Apr 6, 2010 at 4:42 PM, David Winsemius <dwinsem...@comcast.net>wrote:
>
>>
>> On Apr 6, 2010, at 4:03 PM, Abhishek Pratap wrote:
>>
>> Hi David
>>>
>>> Here it is. You can ignore the bio jargon if it sounds confusing.
>>>
>>
>> Sometimes it is essential to have domain details.
>>
>>
>> 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 ...
>>>
>>
>> Looking at this line and the line for "SNP" in the above dataframe I am
>> not seeing that these are exhibiting much similarity in range. There are 10
>> times few observations. What was you plan for the non-matching cases? Did
>> you really mean that you wanted a right outer join?
>>
>> You might get information by trying:
>>
>> length(intersect(data_lane6_snps$SNP, data_lane6_snps_rsid$SNP))
>>
>> That would tell you how many potential matches you might have on the basis
>> of SNP numbers, Although an SNP match might or might not be a full match
>> given the chr matching that is also being specified.
>>
>>
>>
>> $ 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 <dwinsem...@comcast.net>
>>> 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"))
>>>
>>
>> So I am guessing that you really wanted just this:
>>
>> new.data.frame <- merge(df1,df2)
>>
>> ?merge
>>
>> Since the default for merge is: by = intersect(names(x), names(y)), this
>> would have been equivalent to
>>
>> new.data.frame <- merge(df1,df2, by=c("chr", "SNP") )
>>
>> See above regarding the possibility that you have non-congruent SNP
>> labeling problems.
>>
>>
>>
>>
>>
>>> 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]]
>>>
>>> ______________________________________________
>>> R-help@r-project.org 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
>>>
>>>
>>>
>> David Winsemius, MD
>> West Hartford, CT
>>
>>
>
[[alternative HTML version deleted]]
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