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#' Nucleotide variants in example genome samples
#'
#' An example dataset containing 326 variants from 14 genome samples.
#'
#' @format vcfR class object with three sections:
#' \describe{
#' \item{meta}{The metadata for the VCF file including the file format version
#' number}
#' \item{fix}{A character matrix with 326 rows and 8 columns. Contains
#' information on chromosome (CHROM), genome position (POS), reference genome
#' allele (REF), and alternative allele (ALT)}
#' \item{gt}{A character matrix with 326 rows and 15 columns. Presence/absence
#' for each variant defined in fix. Colnames are sample IDs.}
#' }
"vcf"
#' Nucleotide variants in example genome samples with snpeff annotations.
#'
#' An example dataset containing 14 variants from 49 genome samples that has
#' been annotated using snpeff.
#'
#' @format vcfR class object with three sections:
#' \describe{
#' \item{meta}{The metadata for the VCF file including the file format version
#' number}
#' \item{fix}{A character matrix with 14 rows and 8 columns. Contains
#' information on chromosome (CHROM), genome position (POS), reference genome
#' allele (REF), and alternative allele (ALT). Information column (INFO)
#' contains a field called "ANN" which provides the snpeff annotation
#' including predicted functional impact of the variant on the protein
#' function.}
#' \item{gt}{A character matrix with 14 rows and 49 columns. Presence/absence
#' for each variant defined in fix. Colnames are sample IDs.}
#' }
"snpeff_vcf"
#' Phylogenetic tree of example genomes
#'
#' Example unrooted phylogenetic tree.
#'
#' @format An ape phylo object with 14 tips.
"tree"
#' Name of outgroup in the phylogenetic tree.
#'
#' @format Character string.
"outgroup"
#' GFF3 file for example genomes
#'
#' An example of GFF3 formatted genome information.
#'
#' @format A character matrix with 110 rows and 9 columns:
#' \describe{
#' \item{Column 1}{Chromosome}
#' \item{Column 2}{Data source}
#' \item{Column 3}{Feature type}
#' \item{Column 4}{Feature start position}
#' \item{Column 5}{Feature stop position}
#' \item{Column 6}{Score}
#' \item{Column 7}{Strand}
#' \item{Column 8}{Phase}
#' \item{Column 9}{Locus ID}
#' }
"gff"
#' Results from running prewas() on the example data.
#'
#' Output from prewas().
#' results <- prewas::prewas(dna = prewas::vcf,
#' tree = prewas::tree,
#' outgroup = prewas::outgroup,
#' gff = prewas::gff,
#' anc = FALSE)
#'
#' @format List of 5 objects.
#' \describe{
#' \item{allele_mat}{Matrix. Character matrix of nucleotides (alleles).
#' Multiallelic sites represented on multiple lines in the matrix. Dim: 360 x
#' 13. Rows are genomic loci. Columns are samples. Row names include only
#' genomic position and do not have gene information.}
#' \item{bin_mat}{Matrix. Binary matrix (nucleotides stored as 0 or 1).
#' Multiallelic sites represented on multiple lines in the matrix. Alleles in
#' overlapping genes are represented on multiple lines in the matrix. Rownames
#' include genomic position and gene. Dim: 1016 x 13. Rows are genomic loci.
#' Columns are samples.}
#' \item{ar_results}{Data.frame. Dim: 360 x 1. Rows are genomic loci. The
#' column is the major allele at that position. If anc=TRUE, then this object
#' would be a 306 x 2 data.frame where the first column is the ancestral
#' allele at that position inferred from ancestral reconstruction and the
#' second column is the maximum likelihood probability.}
#' \item{dup}{Integer vector. Length = 360. The number refers to the original
#' genomic loci in the VCF file. The occurrence count of the number is one
#' less than the number of alleles. Ex: the 1st genomic locus (Position "1")
#' occurs once in `dup` indicating that this is a biallelic site. In contrast,
#' the 5th genomic locus in the vcf (Position 18) occurs twice indicating that
#' this is a triallelic site (represented in two rows: 18 and 18.1)}
#' \item{gene_mat}{Matrix. Gene-based matrix. Genes with any SNP stored as 1,
#' genes without SNPs stored as 0. Rows are genes. Columns are samples. Dim:
#' 96 x 13.}
#' }
"results"
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