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.
2 answers
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().
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?
The answer is
use
-hmm .../penncnv/lib/hhall.hmm -pfb .../penncnv/lib/hhall.hg18.pfb
•
written
by
bob.obr13n •
Log in to answer this question.
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.