ASAFE: Ancestry Specific Allele Frequency Estimation

Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.

AuthorQian Zhang <qszhang@uw.edu>
Date of publicationNone
MaintainerQian Zhang <qszhang@uw.edu>
LicenseArtistic-2.0
Version1.0.0

View on Bioconductor

Files

ASAFE/DESCRIPTION
ASAFE/NAMESPACE
ASAFE/R
ASAFE/R/algorithm_1snp.R ASAFE/R/algorithm_1snp_wrapper.R ASAFE/R/change_ancestry.R ASAFE/R/draw_allele_given_anc.R ASAFE/R/em.R ASAFE/R/estep.R ASAFE/R/get_errors_1_scenario.R ASAFE/R/get_errors_summary_stats_1_scenario.R ASAFE/R/get_mean_sd_error_anc.R ASAFE/R/get_mean_sd_error_anc_bin.R ASAFE/R/get_results_error.R ASAFE/R/get_scenario_errors.R ASAFE/R/get_true_freqs_1snp.R ASAFE/R/increment_n.R ASAFE/R/mstep.R ASAFE/R/nudge.R ASAFE/R/sample_ancestry.R
ASAFE/README
ASAFE/build
ASAFE/build/vignette.rds
ASAFE/data
ASAFE/data/adm_ancestries_test.rda
ASAFE/data/adm_genotypes_test.rda
ASAFE/data/datalist
ASAFE/inst
ASAFE/inst/ASAFE_Visual.pdf
ASAFE/inst/NEWS
ASAFE/inst/doc
ASAFE/inst/doc/ASAFE.R
ASAFE/inst/doc/ASAFE.Rmd
ASAFE/inst/doc/ASAFE.pdf
ASAFE/inst/scripts
ASAFE/inst/scripts/bgl_then_rfmix.sh
ASAFE/man
ASAFE/man/adm_ancestries_test.Rd ASAFE/man/adm_genotypes_test.Rd ASAFE/man/algorithm_1snp.Rd ASAFE/man/algorithm_1snp_wrapper.Rd
ASAFE/tests
ASAFE/tests/testthat
ASAFE/tests/testthat.R
ASAFE/tests/testthat/test_algorithm_1snp.R
ASAFE/tests/testthat/test_algorithm_1snp_wrapper.R
ASAFE/tests/testthat/test_change_ancestry.R
ASAFE/tests/testthat/test_draw_allele_given_anc.R
ASAFE/tests/testthat/test_em.R
ASAFE/tests/testthat/test_estep.R
ASAFE/tests/testthat/test_get_errors_1_scenario.R
ASAFE/tests/testthat/test_get_errors_summary_stats_1_scenario.R
ASAFE/tests/testthat/test_get_mean_sd_error_anc.R
ASAFE/tests/testthat/test_get_mean_sd_error_anc_bin.R
ASAFE/tests/testthat/test_get_results_error.R
ASAFE/tests/testthat/test_get_scenario_errors.R
ASAFE/tests/testthat/test_get_true_freqs_1snp.R
ASAFE/tests/testthat/test_increment_n.R
ASAFE/tests/testthat/test_mstep.R
ASAFE/tests/testthat/test_nudge.R
ASAFE/tests/testthat/test_sample_ancestry.R
ASAFE/vignettes
ASAFE/vignettes/ASAFE.Rmd

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