User:Timothee Flutre/Notebook/Postdoc/2011/11/16: Difference between revisions
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(Autocreate 2011/11/16 Entry for User:Timothee_Flutre/Notebook/Postdoc) |
(try pkg snpStats) |
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==Entry title== | ==Entry title== | ||
* | |||
* try the R/Bioconductor package [http://www.bioconductor.org/packages/devel/bioc/html/snpStats.html 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)$z.HWE) | |||
Revision as of 13:43, 16 November 2011
 Project name
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Entry title
library(snpStats)
tmp <- matrix(c(1,3,2,1,3,0,1,3,0,1), ncol=2, dimnames=list(paste("snp", 1:5, sep=""), paste("ind", 1:2, sep="")))
tmp
tmp2 <- new("SnpMatrix", t(tmp))
tmp2
summary(tmp2)
print(as(t(tmp2), 'character'))
print(as(t(tmp2), 'numeric'))
Unfortunately, it doesn't seem possible to convert a matrix of characters into SnpMatrix, assuming 1=AA, 2=AB, 3=BB and 0=NC: tmp <- matrix(c("A/A","B/B","A/B","A/A","B/B","","A/A","B/B","","A/A"), ncol=2, dimnames=list(paste("snp", 1:5, sep=""), paste("ind", 1:2, sep="")))
tmp
tmp2 <- new("SnpMatrix", t(tmp))
Thus, in the case where one has a matrix of genotypes obtained by Illumina (whether we have AA or A/A), we need to convert it first to the 1/2/3/0 encoding: tmp <- gsub("A/A", 1, tmp)
tmp <- gsub("A/B", 2, tmp)
tmp <- gsub("B/B", 3, tmp)
tmp <- gsub("^$", 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)
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