Question: Locating enhancers that are mutated
0
gravatar for addyS
3.2 years ago by
addyS0
addyS0 wrote:

Hi,

I have a two dataframes,one containing the genomic co-ordinates of enhancers (column names :#chr,start,end ) and the other containing the SNV position (column names : chr,position).My objective is to obtain those enhancers that are mutated,resultant dataframe should have  the following columns : #chr,start,end,no of mutations.How do I achieve this using gRanges?Also please suggest other R packages if any,with which I can achieve this.

I did in the following way:

grEnhancer<-GRanges(seqnames=enhancer_data$chr,
                    ranges=IRanges(enhancer_data$start,end=enhancer_data$end))
grSNV<-GRanges(seqnames = snvData$X.CHROM,
               ranges = IRanges(snvData$POS,end=snvData$POS))

grSNVhits=intersect(grEnhancer,grSNV)

However this gives me the list of mutations that occur in the provided enhancers.

Please help.

Regards,

Addy

ADD COMMENTlink modified 3.2 years ago by Michael Lawrence11k • written 3.2 years ago by addyS0
Answer: Locating enhancers that are mutated
1
gravatar for Michael Lawrence
3.2 years ago by
United States
Michael Lawrence11k wrote:

Please see ?countOverlaps.

ADD COMMENTlink written 3.2 years ago by Michael Lawrence11k

Thanks a lot. countOverlaps did the job :)

ADD REPLYlink written 3.2 years ago by addyS0
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