allele_count: Allele Count

In andremrsantos/htspop: High-Troughput Sequencing Population Genetics Statistics

Description

Creates an allele count matrix used on other analysis. The structure encapsulates the allele count and number of individual with variant as rows and groups as columns. It allows subsetting ([]), to check dimensions (with dim, nrow, and ncol), and renaming them.

Usage

allele_count(count, n)

allele_count_from_genotype(genotype, groups = NULL)

Arguments

count	Matrix giving the number of alternative (or mutant) alleles with variants as rows and samples as columns.
n	Matrix giving the total number of alleles observed with variants as rows and samples as columns.
genotype	Sample genotype matrix with the variants as rows and samples as column in the format 012, where 0 is the reference homozygous, 1 the heterozygous and 2 the alternative homozygous.
groups	List of sample vector or a single vector of groups used to compute the allele count. When is NULL (default value) it considers all samples as a single group, when is either a vector it considers only the corresponding samples, and when is a list it computes the allele count for each sub-vector.

Value

Allele count matrix

Examples

ac <- allele_count(matrix(0:5, ncol = 2), matrix(rep(6, 6), ncol = 2))

print(ac[1:2, ]) # allows subsetting

nrow(ac)         # number of variants
rownames(ac)     # variants identifier

ncol(ac)         # number of groups
colnames(ac)     # groups names
## From genotype matrix
geno_sample <- matrix(sample(0:2, 100, replace = TRUE), ncol = 10)
ac_matrix_from_genotype(geno_sample)      ## all samples
ac_matrix_from_genotype(geno_sample, 1:5) ## only the first 5
## for three groups
ac_matrix_from_genotype(
  geno_sample,
  list(a = 1:5, b = 3:7, c = 6:10))

andremrsantos/htspop documentation built on May 14, 2020, 11:40 a.m.