Count the number/proportion of present/missing sites in each sample
count_snps(data, missing = FALSE, prop = FALSE)
EIGENSTRAT data object.
Count present SNPs or missing SNPs?
Calculate the proportion instead of counts?
A data.frame object with SNP counts/proportions.
if (FALSE) snps <- eigenstrat(download_data(dirname = tempdir()))
present_count <- count_snps(snps)
#> Error in eval(expr, envir, enclos): object 'snps' not found
missing_count <- count_snps(snps, missing = TRUE)
#> Error in eval(expr, envir, enclos): object 'snps' not found
present_proportion <- count_snps(snps, prop = TRUE)
#> Error in eval(expr, envir, enclos): object 'snps' not found
missing_proportion <- count_snps(snps, missing = TRUE, prop = TRUE)
#> Error in eval(expr, envir, enclos): object 'snps' not found