R: Illumina HumanExome BeadChip SNP Information file
SNPInfo
R Documentation
Illumina HumanExome BeadChip SNP Information file
Description
Contains standard Names and associated genes for the Illumina HumanExome BeadChip
Usage
data(SNPInfo)
Format
A data frame with 247504 observations on the following 2 variables.
Chr
Chromosome
Name
factor: illumina variant names
SKATgene
factor: gene names
Details
There are several non-exonic SNPs included. For these SNPs the 'gene' name is the same as the illumina variant name.
References
Grove ML, Cochran BJ, Haritunians T, Bis JC, Taylor KD, Hansen M, O'Donnell CJ, Rotter JI, Boerwinkle E, CHARGE Exome Chip Genotyping Committee; Best practices and joint calling of the Illumina HumanExome BeadChip: the CHARGE consortium; (Abstract/Program #1445W). Presented at the 62nd Annual Meeting of The American Society of Human Genetics (ASHG), November 7, 2012, San Francisco, CA.
Grove ML, Yu B, Cochran BJ, Haritunians T, Bis JC, Taylor KD, Hansen M, Borecki I, Cupples LA, Fornage M, Gudnason V, Harris T, Katherisan S, Kraaij R, Launer LJ, Levy D, Liu Y, Mosley T, Peloso GM, Psaty BM, Rich SS, Rivadeneira F, Siscovick DS, Smith AV, Uitterlinden A, van Duijn CM, Wilson JG, O'Donnell CJ, Rotter JI, Boerwinkle E. Best practices and joint calling of the Illumina HumanExome BeadChip: the CHARGE consortium. PLoS One [submitted]
Examples
data(SNPInfo)
##summary of the data set:
summary(as.numeric(table(SNPInfo$SKATgene)))
hist(table(SNPInfo$SKATgene),nclass = 300,xlim=c(0,50),
main = "SNPs per gene", xlab ="#SNPs", ylab = "#Genes")