qtl2: basic_summaries – R documentation

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qtl2

basic_summaries

Basic summaries of a cross2 object

Description

Basic summaries of a cross2 object.

Usage

n_ind(cross2)

n_ind_geno(cross2)

n_ind_pheno(cross2)

n_ind_covar(cross2)

n_ind_gnp(cross2)

ind_ids(cross2)

ind_ids_geno(cross2)

ind_ids_pheno(cross2)

ind_ids_covar(cross2)

ind_ids_gnp(cross2)

n_chr(cross2)

n_founders(cross2)

founders(cross2)

chr_names(cross2)

tot_mar(cross2)

n_mar(cross2)

marker_names(cross2)

n_pheno(cross2)

pheno_names(cross2)

n_covar(cross2)

covar_names(cross2)

n_phenocovar(cross2)

phenocovar_names(cross2)

Arguments

cross2

An object of class "cross2", as output by read_cross2(). For details, see the R/qtl2 developer guide.

Value

Variously a number, vector of numbers, or vector of character strings.

Functions

n_ind: Number of individuals (either genotyped or phenotyped)
n_ind_geno: Number of genotyped individuals
n_ind_pheno: Number of phenotyped individuals
n_ind_covar: Number of individuals with covariate data
n_ind_gnp: Number of individuals with both genotype and phenotype data
ind_ids: IDs of individuals (either genotyped or phenotyped)
ind_ids_geno: IDs of genotyped individuals
ind_ids_pheno: IDs of phenotyped individuals
ind_ids_covar: IDs of individuals with covariate data
ind_ids_gnp: IDs of individuals with both genotype and phenotype data
n_chr: Number of chromosomes
n_founders: Number of founder strains
founders: Names of founder strains
chr_names: Chromosome names
tot_mar: Total number of markers
n_mar: Number of markers on each chromosome
marker_names: Marker names
n_pheno: Number of phenotypes
pheno_names: Phenotype names
n_covar: Number of covariates
covar_names: Covariate names
n_phenocovar: Number of phenotype covariates
phenocovar_names: Phenotype covariate names