How to convert segmented aCGH probe-based to gene-based?
1
0
Entering edit mode
6.7 years ago

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?

 

aCGH R gene probe conversion • 1.3k views
ADD COMMENT
2
Entering edit mode
6.7 years ago
arno.guille ▴ 400

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.

ADD COMMENT
0
Entering edit mode

Thanks a million Arno, this worked for me! 

ADD REPLY

Login before adding your answer.

Traffic: 1169 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6