Count the number/proportion of present/missing sites in each sample

Count the number/proportion of present/missing sites in each sample

count_snps(data, missing = FALSE, prop = FALSE)

Arguments

data

EIGENSTRAT data object.

missing

Count present SNPs or missing SNPs?

prop

Calculate the proportion instead of counts?

Value

A data.frame object with SNP counts/proportions.

Examples

if (FALSE) snps <- eigenstrat(download_data(dirname = tempdir()))

present_count <- count_snps(snps)
#> Error in ifelse(is.null(data$group), data$ind, data$group): object 'snps' not found
missing_count <- count_snps(snps, missing = TRUE)
#> Error in ifelse(is.null(data$group), data$ind, data$group): object 'snps' not found

present_proportion <- count_snps(snps, prop = TRUE)
#> Error in ifelse(is.null(data$group), data$ind, data$group): object 'snps' not found
missing_proportion <- count_snps(snps, missing = TRUE, prop = TRUE)
#> Error in ifelse(is.null(data$group), data$ind, data$group): object 'snps' not found