How to get this done in R? Combine rows with the same position.
Hi Guys,
I have a huge table like the one shown below with repeated snp positions. I want to combine all the rows with same position and get the nucleotide counts for each position as shown in the result. Thank you for your help!
df1
seqnames pos nucleotide count
1: chr11 1643082 A 1
2: chr11 1643082 C 3
3: chr11 1643082 T 18
4: chr11 47663948 C 27
5: chr11 47663948 T 2
result
chr11:1643082 T:18,C:3,A:1
chr11 47663948 C:27,T:2
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
R Find which gene a SNP position is in
written by marit.hetland •
-
Parsing a bed file to vcf file in Python
written by alex_gon87 •
-
Help with the perl script to extract mismatches
written by MAPK
-
Get multiple snps coverage (allelic depth) from bam files
written by MAPK
-
R programming: concatenate three character vectors
written by MAPK
-
R programming: search by making key terms
written by MAPK
-
How to select values based on specific condition from the matrix in R
written by MAPK
-
How to do coverage counting for each genomic position in R ?
written by MAPK
-
R programming, column reordering
written by MAPK
-
R programming question: genotyping data table manipulation
written by MAPK
Duplicate How to do coverage counting for each genomic position in R ?.
Specific output is not bioinformatics problem (just read data.table reference manual).
Sorry, Thanks!
Hello MAPK!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
PS: duplicated post, as noted by Pgibas.