updateAF: update allele frequencies function

In GregoryMatesi/RHiddenAncestries: Hidden Ancestries Group R Package

Description

updates allele frequency data in heterogeneous genetic variant data

Usage

updateAF(
  data,
  reference,
  observed,
  pi_target,
  pi_observed = c(NA),
  panel = c("None")
)

Arguments

data	dataframe
reference	Array of character strings. Column names for the ancestries used in the model
observed	Character string. Column name of observed ancestry
pi_target	Numeric vector. Ancestry proportion values for the target ancestry
pi_observed	Numeric vector. Ancestry proportion values for the observed ancestry.
panel	array of character strings. The reference ancestry to be used in the ancestr() function If the user does not have pi_observed values already.

Value

data.frame data with an additional column at the end containing updated allele frequencies.

Author(s)

Gregory Matesi, [e-mail]

Examples

data(ancestryData)
updateAF(data   = ancestryData,
    reference   = c("ref_AF_eur_1000G", "gnomAD_AF_afr"),
    observed    = "gnomAD_AF_afr",
    pi_target   = c(1,0),
    pi_observed = c(.15,.18))

GregoryMatesi/RHiddenAncestries documentation built on July 9, 2020, 7:58 a.m.