algorithm_1snp_wrapper: Wrapper for function algorithm_1snp

In ASAFE: Ancestry Specific Allele Frequency Estimation

Description

Applies the function algorithm_1snp to a particular bi-allelic marker's data stored in matrices alleles and ancestries. Can be used to apply algorithm_1snp to multiple bi-allelic markers.

Usage

algorithm_1snp_wrapper(i, alleles, ancestries)

Arguments

i	Index of marker in matrices alleles and ancestries. This is the index for the marker that we want to apply function algorithm_1snp to.
alleles	Rows: Alleles for individuals' chromosomes ordered e.g. ADM1, ADM1, ..., ADM250, ADM250, where ADMi is the ID for the i-th individual. Cols: Bi-allelic markers. Each allele is either 0 or 1. This is a numeric matrix.
ancestries	Rows: Ancestries for individuals' chromosomes ordered e.g. ADM1, ADM1, ..., ADM250, ADM250, where ADMi is the ID for the i-th individual. Cols: Bi-allelic markers. Each ancestry is either 0, 1, or 2. This is a numeric matrix.

Details

Markers in matrix alleles should be in 1-to-1 correspondence with markers in matrix ancestries. Markers in both matrices should be in the same order.

Value

A character vector with 4 elements. The first element is the Marker ID of the i-th marker in matrices alleles and ancestries. The next 3 elements are ancestry-specific allele frequency estimates of P(Allele 1 | Ancestry 0), P(Allele 1 | Ancestry 1), and P(Allele 1 | Ancestry 2), for the i-th marker in matrices alleles and ancestries.

Author(s)

Qian Zhang

Examples

# adm_ancestries_test is a matrix with
# Rows: Markers
# Columns: Marker ID, individuals' chromosomes' ancestries
# (e.g. ADM1, ADM1, ADM2, ADM2, and etc.)

# adm_genotypes_test is a matrix with
# Rows: Markers
# Columns: Marker ID, individuals' genotypes (a1/a2)
# (e.g. ADM1, ADM2, ADM3, and etc.)

# Making the rsID column row names
row.names(adm_ancestries_test) <- adm_ancestries_test[,1]
row.names(adm_genotypes_test) <- adm_genotypes_test[,1]

adm_ancestries_test <- adm_ancestries_test[,-1]
adm_genotypes_test <- adm_genotypes_test[,-1]

# alleles_list is a list of lists.
# Outer list elements correspond to bi-allelic markers.
# Inner list elements correspond to 250 people's alleles with no delimiter separating alleles.
alleles_list <- apply(X = adm_genotypes_test, MARGIN = 1, FUN = strsplit, split = "/")

# Creates a matrix: Number of alleles (ADM1, ADM1, ..., ADM250, ADM250) x (bi-allelic markers)
alleles_unlisted <- sapply(alleles_list, unlist)

# Change elements of the matrix to numeric, producing a matrix:
# Number of alleles (ADM1, ADM1, ..., ADM250, ADM250) x (bi-allelic markers).
alleles <- apply(X = alleles_unlisted, MARGIN = 2, as.numeric)

# Apply EM algorithm to first bi-allelic marker
algorithm_1snp_wrapper(i = 1, alleles, adm_ancestries_test)

# Apply the EM algorithm to each bi-allelic marker to obtain
# ancestry-specific allele frequency estimates for all markers in
# matrices alleles and ancestries.

adm_estimates_test <- sapply(X = 1:ncol(alleles), FUN = algorithm_1snp_wrapper,
                        alleles = alleles, ancestries = adm_ancestries_test)

adm_estimates_test

ASAFE documentation built on Nov. 8, 2020, 10:59 p.m.