freq: Compute marker allele frequencies

In ytutsunomiya/GHap: Genome-Wide Haplotyping

Compute marker allele frequencies

Description

This function takes a GHap.phase object and computes the allele frequency for each marker.

Usage

  ghap.freq(object, type = "maf",
            batchsize = NULL,
            only.active.samples = TRUE,
            only.active.variants = TRUE,
            verbose = TRUE)

Arguments

object	A GHap object of type phase or plink.
type	A character value indicating which allele frequency to compute. Valid options are minor allele frequency ('maf', default), frequency of allele 0 ('A0') and frequency of allele 1 ('A1').
batchsize	A numeric value controlling the number of variants to be processed at a time (default = nalleles/10).
only.active.samples	A logical value specifying whether only active samples should be used for calculations (default = TRUE).
only.active.variants	A logical value specifying whether only active variants should be included in the output (default = TRUE).
verbose	A logical value specfying whether log messages should be printed (default = TRUE).

Value

The function outputs a numeric vector of the same length of active markers containing allele frequencies based on the active samples.

Author(s)

Yuri Tani Utsunomiya <[e-mail]>
Marco Milanesi <[e-mail]>

Examples

  
# #### DO NOT RUN IF NOT NECESSARY ###
# 
# # Copy phase data in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
#                          format = "phase",
#                          verbose = TRUE)
# file.copy(from = exfiles, to = "./")
# 
# # Copy plink data in the current working directory
# exfiles <- ghap.makefile(dataset = "example",
#                          format = "plink",
#                          verbose = TRUE)
# file.copy(from = exfiles, to = "./")
# 
# ### RUN ###
# 
# # Calculate allele frequency for phase data
# phase <- ghap.loadphase("example")
# q <- ghap.freq(phase, type = 'A0')
# p <- ghap.freq(phase, type = 'A1')
# maf <- ghap.freq(phase, type = 'maf')
# 
# # Calculate allele frequency for plink data
# plink <- ghap.loadplink("example")
# q <- ghap.freq(plink, type = 'A0')
# p <- ghap.freq(plink, type = 'A1')
# maf <- ghap.freq(plink, type = 'maf')

ytutsunomiya/GHap documentation built on Oct. 15, 2024, 5:27 p.m.