hapstats: Haplotype allele statistics

In GHap: Genome-Wide Haplotyping

Haplotype allele statistics

Description

Summary statistics for HapAlleles.

Usage

ghap.hapstats(object,
              alpha = c(1, 1),
              batchsize = NULL,
              only.active.samples = TRUE,
              only.active.alleles = TRUE,
              ncores = 1, verbose = TRUE)

Arguments

object	A GHap.haplo object.
alpha	A numeric vector of size 2 specifying the shrinkage parameters for the expected-to-observed homozygotes ratio. Default is c(1, 1).
batchsize	A numeric value controlling the number of HapAlleles to be processed at a time (default = nalleles/10).
only.active.samples	A logical value specifying whether only active samples should be included in the output (default = TRUE).
only.active.alleles	A logical value specifying whether only active haplotype alleles should be included in the output (default = TRUE).
ncores	A numeric value specifying the number of cores to be used in parallel computations (default = 1).
verbose	A logical value specfying whether log messages should be printed (default = TRUE).

Value

A data frame with columns:

BLOCK	Block alias.
CHR	Chromosome name.
BP1	Block start position.
BP2	Block end position.
ALLELE	Haplotype allele identity.
N	Number of observations for the haplotype.
FREQ	Haplotype frequency.
O.HOM	Observed number of homozygotes.
O.HET	Observed number of heterozygotes.
E.HOM	Expected number of homozygotes.
RATIO	Shrinkage expected-to-observed ratio for the number of homozygotes.
BIN.logP	log10(1/P) or -log10(P) for Hardy-Weinberg equilibrium assuming number of homozygotes follows a Binomial distribution.
POI.logP	log10(1/P) or -log10(P) for Hardy-Weinberg equilibrium assuming number of homozygotes follows a Poisson distribution.
TYPE	Category of the HapAllele: "SINGLETON" = single allele of its block; "ABSENT" = the frequency of the allele is 0; "MINOR" = the least frequent allele of its block (in the case of ties, only the first allele is marked); "MAJOR" = the most frequent allele of its block (ties are also resolved by marking the first allele); "REGULAR" = the allele does not fall in any of the previous categories. Categories "SINGLETON", "MINOR" and "MAJOR" only apply for blocks where frequencies sum to 1.

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 = "./")
# 
# ### RUN ###
# 
# # Load data
# phase <- ghap.loadphase("example")
# 
# # Generate blocks of 5 markers
# blocks <- ghap.blockgen(phase, windowsize = 5,
#                         slide = 5, unit = "marker")
# 
# # Haplotyping
# ghap.haplotyping(phase = phase, blocks = blocks, outfile = "example",
#                  binary = T, ncores = 1)
# 
# # Load haplotype genotypes using prefix
# haplo <- ghap.loadhaplo("example")
# 
# ### RUN ###
# 
# # Subset
# ids <- which(haplo$pop == "Pure1")
# haplo <- ghap.subset(haplo, ids = ids,
#                      variants = haplo$allele.in,
#                      index = TRUE)
# 
# # Compute haplotype statistics
# hapstats <- ghap.hapstats(haplo)

GHap documentation built on July 2, 2022, 1:07 a.m.