setupSNP {SNPassoc} | R Documentation |
Convert columns in a dataframe to class 'snp'
Description
setupSNP
Convert columns in a dataframe to class 'snp'
summary.setupSNP
gives a summary for an object of class 'setupSNP' including
allele names, major allele frequencie, an exact thest of Hardy-Weinberg
equilibrium and percentage of missing genotypes
Usage
setupSNP(data, colSNPs, sort = FALSE, info, sep = "/", ...)
Arguments
data |
dataframe containing columns with the SNPs to be converted |
colSNPs |
Vector specifying which columns contain SNPs data |
sort |
should SNPs be sorted. Default is FALSE |
info |
if sort is TRUE a dataframe containing information about the SNPs regarding their genomic position and the gene where they are located |
sep |
character separator used to divide alleles in the genotypes |
... |
optional arguments |
Value
a dataframe of class 'setupSNP' containing converted SNP variables. All other variables will be unchanged.
References
JR Gonzalez, L Armengol, X Sole, E Guino, JM Mercader, X Estivill, V Moreno. SNPassoc: an R package to perform whole genome association studies. Bioinformatics, 2007;23(5):654-5.
See Also
Examples
data(SNPs)
myDat<-setupSNP(SNPs,6:40,sep="")
#sorted SNPs and having genomic information
data(SNPs.info.pos)
myDat.o<-setupSNP(SNPs,6:40,sep="",sort=TRUE, info=SNPs.info.pos)
# summary
summary(myDat.o)
# plot one SNP
plot(myDat,which=2)