I'm trying to combine aCGH with genes filtered after an RNA-seq run.
Simplified, this is what the data is organized like:
File1, aCGH: (4 columns)
chromosome no. - start position - end position - probe strength.
File2, genes of interest (3 columns)
chromosome no. - position - gene name
I would like to see if my genes are covered by the aCGH probes (that is, the gene position in file2 is within start and stop positions in file1, with the corresponding chromosome correct), and if so - return the probe strength value for the corresponding probe. I tried to construct a pivot table in excel, but that didn't do it. The number of probes are of course, high. I have about 5000 genes of interest.
Is it some easy way to do this? My R is limited, so if you can come up with an alternative I would be very happy!
/Hubertus
Simplified, this is what the data is organized like:
File1, aCGH: (4 columns)
chromosome no. - start position - end position - probe strength.
File2, genes of interest (3 columns)
chromosome no. - position - gene name
I would like to see if my genes are covered by the aCGH probes (that is, the gene position in file2 is within start and stop positions in file1, with the corresponding chromosome correct), and if so - return the probe strength value for the corresponding probe. I tried to construct a pivot table in excel, but that didn't do it. The number of probes are of course, high. I have about 5000 genes of interest.
Is it some easy way to do this? My R is limited, so if you can come up with an alternative I would be very happy!
/Hubertus
