Nothing
`is.snp` <-
function(data,sep){
j<-1
if (!is.data.frame(data)) stop("Data is not a data.frame object. \n")
if (any(apply(data,2,is.factor))) stop("Some data columns are factors. \n")
if (ncol(data)==1) stop("There is only one SNP, is not possible to perform a haplotype analysis. \n")
col.rm<-NULL
for (j in 1:ncol(data))
{
if (sum(is.na(data[,j]))==nrow(data)) stop("At least one SNP values are all missings. \n")
geno<-genotype(data[,j],sep=sep)
a<-allele(geno)
if (length(attr(a,"allele.names"))==1){
warning("At least one SNP is homozygous for everyone.\n")
#col.rm<-c(col.rm,j)
}
alleles<- sort(attr(a,"allele.names"))
if (length(alleles)>2) stop("SNP data is not biallelic.\n")
if ( sum(geno[!is.na(geno)]%in%c(paste(alleles[1],alleles[1],sep=sep),paste(alleles[1],alleles[2],sep=sep),
paste(alleles[2],alleles[1],sep=sep),paste(alleles[2],alleles[2],sep=sep)))!=nrow(data)-sum(is.na(geno)))
stop("SNP data is not correct.\n")
}
#data<-data[,-col.rm]
}
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