Description Usage Arguments Details Value Author(s) Examples

View source: R/algorithm_1snp_wrapper.R

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.

1 | ```
algorithm_1snp_wrapper(i, alleles, ancestries)
``` |

`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. |

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.

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.

Qian Zhang

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | ```
# 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
``` |

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