snpRdata-class | R Documentation |
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.
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.
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.
William Hemstrom
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