snpRdata-class: Storage class for snpR data and calculated statistics.

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Storage class for snpR data and calculated statistics.

Description

The snpRdata class stores both raw genotype data, sample and locus specific metadata, useful data summaries, repeatedly internally used tables, calculated summary statistics, and smoothed statistic data. Used by most snpR functions.

Details

The snpRdata class is built to contain SNP genotype data for use by functions in the snpR package. It also stores sample and locus specific metadata, genomic summary information, and any results from most snpR functions. Results can be gathered using get.snpR.stats. Genotypes are stored in the "character" format, as output by format_snps().

For more information, see import.snpR.data, the constructor function for this object class.

Slots

sample.meta

data.frame containing sample metadata

snp.meta

data.frame containing snp metadata

facet.meta

data.frame containing snp metadata for the geno.tables (in the order of snps in that data)

mDat

character, missing data key

snp.form

numeric, number of characters per genotype (not really used)

geno.tables

list containing three matrices: gs (genotype counts), as (allele counts), and wm (missing counts)

facets

character, vector of tabulated facets

facet.type

character, types of each tabulated facet.

stats

data.frame, all calculated single-snp non-pairwise stats.

window.stats

data.frame, all calculated window non-pairwise stats.

pairwise.stats

data.frame, all calculated pairwise single snp stats.

pairwise.window.stats

data.frame, all calculated window pairwise stats.

sample.stats

data.frame, all calculated single sample stats.

pop.stats

data.frame, all calculated population level summary stats.

pairwise.LD

nested list of matrices, all calculated pairwise LD stats.

window.bootstraps

data.frame, all calculated bootstraps

sn

list, contains sn formatted data if calculated

calced_stats

list, contains information on what statistics have been calculated for which facets

allele_frequency_matrices

list of matrices, allele frequency matrices if calculated

genetic_distances

list of matrices, genetic distance matrices if calculated

other

list, contains other miscellaneous calculated statistics that do not fit cleanly elsewhere.

Author(s)

William Hemstrom

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.