Package 'hmmibdr'

Title: HMM Identity by Descent
Description: Wrapper for HMMIBD in Rcpp.
Authors: OJ Watson
Maintainer: Oliver Watson <[email protected]>
License: MIT + file LICENCE
Version: 0.2.0
Built: 2024-11-06 04:11:10 UTC
Source: https://github.com/OJWatson/hmmibdr

Help Index

The Real McCOIL categorical method function

Description

This function triggers the c code for the categorical method

Usage

hmm_ibd(
  input_file,
  output_file,
  allele_freqs = NULL,
  genotypes_sec_pop = NULL,
  allele_freqs_sec_pop = NULL,
  max_fit_iterations = NULL,
  exclude_ids = NULL,
  analysis_ids = NULL,
  num_gens = NULL,
  overwrite = FALSE,
  fract_only = FALSE,
  eps = 0.001,
  min_inform = 10,
  min_discord = 0,
  max_discord = 1,
  nchrom = 14,
  min_snp_sep = 5,
  rec_rate = 7.4e-07,
  cache = TRUE
)

Arguments

input_file

File of genotype data. See below for format.
output_file

Output file name. Two output files will be produced, with ".hmm.txt" and ".hmm_fract.txt" appended to the supplied name.
allele_freqs

File of allele frequencies for the sample population. Format: tab-delimited, no header, one variant per row. Line format: <chromosome (int)> <position (bp, int)> <allele 1 freq> <all 2 freq> ... The genotype and frequency files must contain exactly the same variants, in the same order. If no file is supplied, allele frequencies are calculated from the input data file.
genotypes_sec_pop

File of genotype data from a second population; same format as for -i. (added in 2.0.0)
allele_freqs_sec_pop

File of allele frequencies for the second population; same format as for -f. (added in 2.0.0)
max_fit_iterations

Maximum number of fit iterations (defaults to 5).
exclude_ids

File of sample ids to exclude from all analysis. Format: no header, one id (string) per row. (Note: b stands for "bad samples".)
analysis_ids

File of sample pairs to analyze; all others are not processed by the HMM (but are still used to calculate allele frequencies). Format: no header, tab-delimited, two sample ids (strings) per row. (Note: "g" stands for "good pairs".)
num_gens

Cap on the number of generations (floating point). Sets the maximum value for that parameter in the fit. This is useful if you are interested in recent IBD and are working with a population with substantial linkage disequilbrium. Specifying a small value will force the program to assume little recombination and thus a low transition rate; otherwise it will identify the small blocks of LD as ancient IBD, and will force the number of generations to be large.
overwrite

Boolean detailing if output files already exist, should they be overwritten. Deafult = FALSE
fract_only

Boolean detailing whether to rturn just the fract. Default = FALSE
eps

Numeric for error rate in genotype calls. Default = .001
min_inform

Minimum number of informative sites in a pairwise. Default = 10
min_discord

Minimum discordance in comparison. Default = 0. Set > 0 to skip identical pairs
max_discord

Maximum discordance in comparison. Default = 1. Set < 1 to skip unrelated pairs
nchrom

Number of chromosomes. Default = 14 for falciparum
min_snp_sep

Minimum snp distance, i.e. skip next snp(s) if too close to last one. Default = 5 (bp)
rec_rate

Recombination rate. Default = 7.4e-7. (7.4e-5 cM/bp or 13.5 kb/cM Miles et al, Genome Res 26:1288-1299 (2016))
cache

Should files created by hmm_ibd be cached (i.e. not deleted). Default = TRUE, i.e. keep the files

Value

return list of summary data frames of hmmIBD output

hmmIBD

Description

hmmIBD implementation from https://github.com/glipsnort/hmmIBD

Usage

hmmibd_c(param_list)

Arguments

param_list

A list of parameters created with hmm_ibd

Details

hmmibd_c implements hidden Markov model for detecting segments of shared ancestry (identity by descent) in genetic sequence data.

Wrapper for HMMIBD in Rcpp

Description

Wrapper for HMMIBD in Rcpp

Details

Rcpp implementation of THMMIBD

References

https://github.com/glipsnort/hmmIBD