Hi I have a a data frame with chromosome and position columns (for example chr1 12000). I have extracted the transcripts with the function transcripts() from Genomic Features. I would like to check if some position are in some transcripts. Is there a function in GenomicRanges that could help me?

Thank you

Riccardo

Create a GRanges from the data.frame, then see ?findOverlaps. Something like:

overTx <- makeGRangesFromDataFrame(df) %over% tx

Thank, could you explain me what is %over%?