Hello

I want to estimate the correlation between two peak data for Histone modification chip seq data using R. I have a bed file and how can I get the information about the mean,std deviation so that I can get the correlation coefficient between several data sets and also plot that.

How do I get the vector for bed file.

Thanks BCW

Thanks a lot. This helped.

Hi

I installed the GMD package and worked on the example datasets. But they did not explain about how they got the data(infact referred other paper),meaning usually the chip seq data has chromosome,start and end position details. They started with the matrices that already had the distance coefficients for all 5 histone modificaion files in file called chipseq_mES.

My question is how do I convert my data (bed file) into the vectors of the distance/correlation coefficients.Please share any comments if you have got on workflow of how to get started with correlation btw histone chipseq data.