How to plot B-allele frequency and Log R ratio using R

Question

[Raj]

Hi i am new to R as well as microarray data analysis. I processed illumina array data using genomestudio and got the B-allele frequency and Log R ratio. Now i am trying to plot these values for all the chromosomes in a single plot using R. But i am unable to do it. Please if you guys have some suggestion then let me know. Thanks.

[Raj]

Thanks for the information

Answer 1

[Michael]

See Drawing Chromosome Ideograms With Data one of the methods listed there should work for you.

Answer 2

[bernatgel]

To plot data along the genome you can use karyoploteR. It's in Bioconductor (so you can install it with BiocManager::install(karyoploteR) and can plot almost anything on almost any genome.

There's a tutorial and examples page that contains a specific example on how to plot BAF and LRR values from SNP array that produces a plot like this:

You can customize the image in many ways to adjust it to your needs.