Hi everyone!

I have a question that I would really appreciate it if you help me out, please!

I have a list of data that I would like to know how to find out the gene's names in the regions. The dataset which is a text file has the following format:

Segment               Count              First                 End
0                      258               1_1960674             1_2013259
1                      85                1_3057480             1_3257840
2                      185               1_3340901             1_3783903
3                      215               1_209363247           1_209995470

In this dataset, the first column is the number of segment, the second column is representing the number of SNPs per segment, and the third and fourth columns are representing the smallest and largest SNPs number for each segment. I should note that the values of the third and fourth columns are the combination of the chromosome number and its position Now, how can I understand the gene names in these regions?

Thank you very much

You could try to use annotatePeakInBatch to annotate the regions by setting the parameter output to "overlapping" https://www.rdocumentation.org/packages/ChIPpeakAnno/versions/3.6.5/topics/annotatePeakInBatch

For more information, please refer to http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

Best regards,

Julie