adjAF: adjAF

In hendriau/Summix: Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data

adjAF

Description

Adjusts allele frequencies for heterogeneous populations in genetic data given proportion of reference groups

Usage

adjAF(
  data,
  reference,
  observed,
  pi.target,
  pi.observed,
  adj_method = "average",
  N_reference = NULL,
  N_observed = NULL,
  filter = TRUE
)

Arguments

data	dataframe of unadjusted allele frequency for observed group, K reference group allele frequencies for N SNPs
reference	character vector of the column names for K reference groups.
observed	character value for the column name of observed data group
pi.target	numeric vector of the mixture proportions for K reference groups in the target individual or group.
pi.observed	numeric vector of the mixture proportions for K reference groups in the observed group.
adj_method	user choice of method for the allele frequency adjustment: options "average" and "leave_one_out" are available. Defaults to "average".
N_reference	numeric vector of the sample sizes for each of the K reference groups.
N_observed	numeric value of the sample size of the observed group.
filter	sets adjusted allele frequencies equal to 1 if > 1, to 0 if > -.005 and < 0, and removes adjusted allele frequencies < -.005.

Value

pi: table of input reference groups, pi.observed, and pi.target

observed.data: name of the data column for the observed group from which adjusted allele frequency is estimated

Nsnps: number of SNPs for which adjusted AF is estimated

adjusted.AF: data frame of original data with an appended column of adjusted allele frequencies

effective.sample.size: The sample size of individuals effectively represented by the adjusted allele frequencies

Author(s)

Adelle Price, [e-mail]

Hayley Wolff, [e-mail]

Audrey Hendricks, [e-mail]

References

https://github.com/hendriau/Summix2

See Also

https://github.com/hendriau/Summix2 for further documentation.

Examples

data(ancestryData)
adjusted_data<-adjAF(data   = ancestryData,
    reference  = c("reference_AF_afr", "reference_AF_eur"),
    observed    = "gnomad_AF_afr",
    pi.target   = c(1, 0),
    pi.observed = c(.85, .15),
    adj_method = 'average',
    N_reference = c(704,741),
    N_observed = 20744,
    filter = TRUE)
adjusted_data$adjusted.AF[1:5,]

hendriau/Summix documentation built on Nov. 13, 2024, 6:53 a.m.