ptl_mapping: A Workflow That Maps PTLs, QTLs, Returns involved Objects,...

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 Workflow That Maps PTLs, QTLs, Returns involved Objects, Embed Caching Fetures

Description

This function is a workflow that encapsulated many functions of the R package 'ptlmapper'. It aggregates parameter values, inputs and outputs of the call to the R package 'ptlmapper' function. The resulting data structure could be cache on the file system. It is useful to massivelly save multiple call to 'ptl_scan' and 'rqtl_launch' function, for example in a complex design.

Usage

ptl_mapping(genodata, cells, bckg, nb_perm = 20, bin_width = NULL,
  nb_dim = 0, errs = 0.05, nb_bin = 100, nb_moments = 4,
  min_prop = 0.1, ptl_mapping_filename = NULL, COMPUTE_KD_MATRIX = TRUE,
  COMPUTE_MM_MATRIX = TRUE, DO_KANTO = TRUE, DO_MMOMENTS = TRUE,
  DO_RQTL = TRUE, CLEAN_OBJECT = FALSE, SKEWNESS_AND_KURTOSIS = FALSE)

Arguments

genodata	A matrix describing the genotype of individuals.
cells	A list of vector of integer (single cell values).
bckg	Vector of character describing the individuals as they are describe in genodata.
nb_perm	An integer that specifies the number of permuation to do.
bin_width	An integer specifying the width of the bin to use.
nb_dim	An integer that specifies the number of dimension of the MDS space to explore.
errs	A vector of integer (error) that will be used to compute threshold from the permutation test.
nb_bin	An integer specifying the number of to use.
nb_moments	An integer specifying the number of moments to compute.
min_prop	A numeric specifying the minimal proportion of each parental allele under which a marker is discard from the analysis.
ptl_mapping_filename	A character string that specifies the file to save the 'ptl_mapping' results.
COMPUTE_KD_MATRIX	A boolean that specifies if 'kd_matrix' needs to be computed.
COMPUTE_MM_MATRIX	A boolean that specifies if 'mm_matrix' needs to be computed.
DO_KANTO	A boolean that specifies if 'ptl_scan' with method="kanto" needs to be performed.
DO_MMOMENTS	A boolean that specifies if 'ptl_scan' with method="mmoments" needs to be performed.
DO_RQTL	A boolean that specifies if 'rqtl_launch' needs to be called.
CLEAN_OBJECT	A boolean that specifies if 'ptl_mapping' results needs to be cleaned.
SKEWNESS_AND_KURTOSIS	A boolean that specifies if skewness and kurtosis QTl need to be scanned.

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