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.

Author
Qian Zhang <qszhang@uw.edu>
Date of publication
None
Maintainer
Qian Zhang <qszhang@uw.edu>
License
Artistic-2.0
Version
1.0.0

View on Bioconductor

Man pages

adm_ancestries_test
Ancestries of 250 admixed individuals at 6 SNPs
adm_genotypes_test
Genotypes of 250 admixed individuals at 6 markers
algorithm_1snp
Estimate ancestry-specific allele frequencies for 1 marker...
algorithm_1snp_wrapper
Wrapper for function algorithm_1snp

Files in this package

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