How to convert segmented aCGH probe-based to gene-based?

Question

[sjorsvanheuveln]

I'm looking for the easiest method in R to convert my segmented aCGH probes into log ratios per gene (they're not called). Furthermore I only have chromosome number and start position available. What is the best way to achieve this goal?

Answer 1

[arno.guille]

Hello,

Here is my solution:

I use bedtools intersect to find overlaps between segdata output and genes coordinates (refseq from ucsc).

bedtools intersect -a segData.bed -b genes.bed -loj > overlap.bed

Then with R

res = read.table("overlap.bed",sep="\t",header=F)
abs_max = tapply(res$V4,as.character(res$V8),function(x){ x[which.max(abs(x))] })

As you can see, I take the maximum in absolute value

• res$V4 correspond to the log2ratio value
• res$V8 correspond to the Symbol

If you need more help, let me know.

[sjorsvanheuveln]

Thanks a million Arno, this worked for me!