ptl_scan: A Function That Scans Genome to Detect PTLs

In fchuffar/ptlmapper: Useful genetic tool allowing to discriminate individuals by comparing the distribution of their phenotype and to map the genetic loci responsible for specific distributions

A Function That Scans Genome to Detect PTLs

Description

This function scans genome to detect PTLs. It determines with the Kaiser criterion how many dimensions of the MDS are relevants for canonical analysis ('eig_to_scan'). If nb_dim=0, a z-core criterion id used to determine with how many dimensions the canonical analysis gives the best result (to fixe 2 <= nb_dim <= eig_to_scan). If nb_dim=NULL, 'nb_dim' is automatically set to eig_to_scan. If nb_dim>0 the canonical analysis is performed used provided 'nb_dim'. In this case, keep attention to the fact that a high value of 'nb_dim' introduce a lot of degree of freedom in your canonical analysis. The number of dimension 'nb_dim' needs to be __substantially__ smaller than the size of your population. The permutations batch uses 'ptl_scan' function with the 'nb_dim' value as the one provided by the initial ptl_scan call.

Usage

ptl_scan(pheno_matrix, genodata_ptl, nb_perm = 0, nb_dim = 0,
  min_prop = 0.1, SHOW_PERM_PROG = TRUE, perm_prog_freq = 5,
  method = "kanto")

Arguments

pheno_matrix	The phenotype matrix (Kantorivitch distance matrix or multivariate moments matrix, according to 'method').
genodata_ptl	The preprocessed genodata. Typically output of 'preprocess_genodata' function.
nb_perm	An integer that specifies the number of permuation to do.
nb_dim	An integer that specifies the number of dimension of the MDS space to explore.
min_prop	A numeric specifying the minimal proportion of each parental allele under which a marker is discard from the analysis.
SHOW_PERM_PROG	A boolean specifying if permutation progression need to to report on console.
perm_prog_freq	An integer specifying the frequency of the permution progression reporting.
method	A character string in c("kanto", "mmoments") that specify the method to use to characterize phenotypic distribution. Default is our favourite: "kanto"!

fchuffar/ptlmapper documentation built on March 27, 2024, 3:28 p.m.