Pfb File For Cnv Analysis Using Illumina 610 Quad V1 Arrays

Question

[Neilfws]

I'm looking at the genoCN package from Bioconductor. The genoCNV() function takes an argument, pBs, which I believe refers to "population frequency of allele B", or PFB.

I'm trying to find a PFB file for the Illumina 610 Quad V1 array platform. The only reference to it that I've found is in this paper which states: "For the samples genotyped on the 610-Quad BeadChips, we used the hh550_610.hg18 pfb and gc model files separately provided by Dr. Kai Wang".

Does anyone know whether this PFB file is available for download anywhere? The pennCNV contains a couple of PFB files (hhall and hh550), but not a 610 file. It also includes a script, compile_pfb.pl, which seems to run using my files (BeadStudio output), but I'm not sure if this is the correct usage.

[Neilfws]

I may have answered my own question, in that the hhall pfb file seems to contain at least some of the SNPs from my 610 intensity files - but still interested in any answers.

Answer 1

[Neilfws]

So, I have answered my own question and here's my solution.

First, read the hhall.hg18.pfb file from PennCNV into R:

pfb <- read.table("hhall.hg18.pfb", sep = "\t", header = T, stringsAsFactors = F)

Then, read in a Bead Studio data file:

mydata <- read.table("myfile.txt", skip = 10, 
                     header = T, sep = "\t", 
                     stringsAsFactors = F)

Extract, say Chr22 from the data and sort by position:

mydata.22 <- mydata[mydata$Chr == 22,]
mydata.22 <- mydata.22[sort.list(mydata.22$Position),]

Match column SNP.Name (mydata) with column Name (pfb) and add PFB to mydata:

m <- match(mydata.22$SNP.Name, pfb$Name)
mydata.22$pfb <- pfb[m, "PFB"]

Data frame mydata.22 now has columns Log.R.Ratio, B.Allele.Freq and pfb, used for input to genoCNV().

[Neilfws]

and I guess I have to select my own answer as the best one :)

[bob.obr13n]

Hi

I am having the same problem - just started with penncnv - - are there any .pfb files for the 610-quad ?- I am not sure I undersand what you have done above could you explain please?

Answer 2

[bob.obr13n]

The answer is

use

-hmm .../penncnv/lib/hhall.hmm -pfb .../penncnv/lib/hhall.hg18.pfb

[Neilfws]

Not the answer when using Bioconductor/genoCN. Suggest you read the question next time.