User:Timothee Flutre/Notebook/Postdoc/2011/11/16

Entry title

• try the R/Bioconductor package snpStats:

library(snpStats)
tmp <- matrix(c(1,3,2,1,3,0,1,3,0,1), ncol=2, dimnames=list(paste("snp", 1:5, sep=""), paste("ind", 1:2, sep="")))
tmp
tmp2 <- new("SnpMatrix", t(tmp))
tmp2
summary(tmp2)
print(as(t(tmp2), 'character'))
print(as(t(tmp2), 'numeric'))

Unfortunately, it doesn't seem possible to convert a matrix of characters into SnpMatrix, assuming 1=AA, 2=AB, 3=BB and 0=NC:

tmp <- matrix(c("A/A","B/B","A/B","A/A","B/B","","A/A","B/B","","A/A"), ncol=2, dimnames=list(paste("snp", 1:5, sep=""), paste("ind", 1:2, sep="")))
tmp
tmp2 <- new("SnpMatrix", t(tmp))

Thus, in the case where one has a matrix of genotypes obtained by Illumina (whether we have AA or A/A), we need to convert it first to the 1/2/3/0 encoding:

tmp <- gsub("A/A", 1, tmp)
tmp <- gsub("A/B", 2, tmp)
tmp <- gsub("B/B", 3, tmp)
tmp <- gsub("^$", 0, tmp)
tmp <- matrix(as.numeric(tmp), ncol=ncol(tmp), dimnames=list(rownames(tmp), colnames(tmp)))
tmp
tmp2 <- new("SnpMatrix", t(tmp))
tmp2
summary(tmp2)

Then, one can easily look at summary statistics, eg. the histogram of minor allele frequencies, of z-score for HWE, etc, and filter data accordingly:

hist(col.summary(tmp2)$MAF)
hist(col.summary(tmp2)$z.HWE)