SNPInfo: Illumina HumanExome BeadChip SNP Information file

Description Usage Format Details References Examples

Description

Contains standard Names and associated genes for the Illumina HumanExome BeadChip

Usage

1
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

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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")

Example output

Loading required package: Matrix
Loading required package: coxme
Loading required package: survival
Loading required package: bdsmatrix

Attaching package: 'bdsmatrix'

The following object is masked from 'package:base':

    backsolve

Loading required package: CompQuadForm
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  1.000   1.000   5.000   9.191  12.000 849.000 

skatMeta documentation built on Sept. 12, 2016, 12:52 p.m.