BayHap (version 1.0.1)

BayHap-internal: Internal BayHap functions

Description

allele: function from package genetics. Extract the specified allele(s) as a character vector or a 2 column matrix. Author: Gregory R. Warnes allele.names: function from package genetics: extract the set of allele names. Author: Gregory R. Warnes chain.import: Read an MCMC sequence from an external file and add it to the session lists of sequences. The original function belongs to the boa package and is named 'boa.chain.import'. Original version by Brian J. Smith. Adapted version by Raquel Iniesta boa.plot.acf.ad:Creates a single plot of the lag autocorrelations for a specified parameter. The original function belongs to the boa package and is named 'boa.plot.acf'. Original version by Brian J. Smith. Adapted version by Raquel Iniesta genotype: function from package genetics: creates a genotype object. Authors: Gregory R. Warnes and Friedrich Leisch. expectedGenotypes:from package genetics: constructs expected genotypes according to known allele variants, which can be quite tedious with large number of allele variants. It can handle different level o ploidy. Author: Gregor Gorjanc haplo.list: List all the haplotypes compatible with a given genotype. Author: Raquel Iniesta haplo.list.all: Lists all the possible haplotypes for a given number of biallelic loci. Author: Raquel Iniesta haplo.pairs: List haplotypes pairs compatible with each genotype of a given sample. Author: Raquel Iniesta import: Import data from an ASCII text file. The variables and iterations should appear in the columns and rows, respectively, of the file. The variable names must be given in the first row. The iteration numbers are taken from the the column entitled "iter" (case-sensitive), if it exists; otherwise, the numbers 1..n are used, where n is the number of rows. The columns may be separated by white space or tabs. The original function belongs to the boa package and is named 'boa.importASCII'. Original version by Brian J. Smith. Adapted version by Raquel Iniesta is.genotype: from package genetics: return 'TRUE' if 'x' is of class 'genotype'. Authors: Gregory R. Warnes and Friedrich Leisch. is.locus: from package genetics : test whether an object is a member of the class 'locus'. Authors: Gregory R. Warnes and Friedrich Leisch. is.snp: Test if data entered as SNP are adequate to be analized. Author: Raquel Iniesta make.dummies: Makes dummies variables for each categorical covariate of the selected model. Author: Raquel Iniesta survival: Creates the response object needed in formula for the survival model. Author: Raquel Iniesta permutations and combinations:from package genetics and gtools respectively: Enumerate the possible permutations and combinations of a specified size from the elements of a vector. Original version in the package gtools by Bill Venables. Permutations extended to handle 'repeats.allowed' by Gregory R. Warnes in the package genetics.

Usage

allele(x, which = c(1, 2)) allele.names(x) chain.import(x, type = "ASCII",keep.rares.chain=FALSE)  boa.plot.acf.ad(x, pname, annotate = boa.par("legend"))  genotype(a1, a2 = NULL, alleles = NULL, sep = "/", remove.spaces = TRUE,  reorder = c("yes", "no", "default", "ascii", "freq"), allow.partial.missing = FALSE,  locus = NULL)  expectedGenotypes(x, alleles = allele.names(x), ploidy = 2, sort = TRUE, haplotype = FALSE)   haplo.list(nlocus,haplo1,haplo2,hetero,nhetero,rows,cols) haplo.list.all(nlocus)  haplo.pairs(geno) import(filename, path = NULL)  is.genotype(x) is.locus(x) make.dummies(covariate) survival(time, status) permutations(n, r, v = 1:n, set = TRUE, repeats.allowed = FALSE)

Details

These functions are not to be called by the user.