Description Usage Arguments Value Examples
View source: R/alleles_recessive_test.R
test for enrichment of inherited variants in multiple populations
1 | enrichment_multiple_populations(freqs, counts, cohort_n, autozygosity = 0)
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freqs |
list of frequency estimates for each ExAC population. |
counts |
list of counts of biallelically inherited genotypes in a gene for: 1) biallelic_lof - inherited Lof/LoF variants, 2) lof_func - ninherited Lof/Func variants, 3) biallelic_func inherited func/func variants. 3) biallelic_syn inherited synonymous/synonymous variants. |
cohort_n |
list of number of probands in each population. |
autozygosity |
rate of autozygosity in the cohort being investigated. |
a list of P values from tests across the populations, under LoF and functional tests.
1 2 3 4 5 6 | freqs = list("AFR"=list("lof"=0.01, "functional"=0.1,"synonymous"=0.3),
"EAS"=list("lof"=0.02, "functional"=0.1,"synonymous"=0.3))
counts = list("biallelic_lof"=4, 'biallelic_func'=6, 'lof_func'=3,"biallelic_syn"=5)
cohort_n = list("AFR"=50, "EAS"=150)
autozygous_rate = 0.005
enrichment_multiple_populations(freqs, counts, cohort_n, autozygous_rate)
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