R/data.R

In cubar: Codon Usage Bias Analysis

#' human mitochondrial CDS sequences
#'
#' CDSs of 13 protein-coding genes in the human mitochondrial genome extracted from ENSEMBL Biomart
#'
#' @format a DNAStringSet of 13 sequences
#' @source <https://www.ensembl.org/index.html>
#' @examples
#' head(human_mt)
"human_mt"


#' yeast CDS sequences
#'
#' CDSs of all protein-coding genes in Saccharomyces_cerevisiae
#'
#' @format a DNAStringSet of 6600 sequences
#' @source <https://ftp.ensembl.org/pub/release-107/fasta/saccharomyces_cerevisiae/cds/Saccharomyces_cerevisiae.R64-1-1.cds.all.fa.gz>
#' @examples
#' head(yeast_cds)
"yeast_cds"


#' Half life of yeast mRNAs
#'
#' Half life of yeast mRNAs in Saccharomyces_cerevisiae calculated from rRNA-deleted total RNAs by Presnyak et al.
#'
#' @format a data.frame with 3888 rows and three columns:
#' \describe{
#' \item{gene_id}{gene id}
#' \item{gene_name}{gene name}
#' \item{half_life}{mRNA half life in minutes}
#' }
#' @source <https://doi.org/10.1016/j.cell.2015.02.029>
#' @references Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, et al. 2015. Codon optimality is a major determinant of mRNA stability. Cell 160:1111-1124.
#' @examples
#' head(yeast_half_life)
"yeast_half_life"


#' yeast mRNA expression levels
#'
#' Yeast mRNA FPKM determined from rRNA-depleted (RiboZero) total RNA-Seq libraries. RUN1_0_WT and RUN2_0_WT (0 min after RNA Pol II repression) were averaged and used here.
#'
#' @format a data.frame with 6717 rows and three columns:
#' \describe{
#' \item{gene_id}{gene ID}
#' \item{gene_name}{gene name}
#' \item{fpkm}{mRNA expression level in Fragments per kilobase per million reads}
#' }
#' @source <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57385>
#' @references Presnyak V, Alhusaini N, Chen YH, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, et al. 2015. Codon optimality is a major determinant of mRNA stability. Cell 160:1111-1124.
#' @examples
#' head(yeast_exp)
"yeast_exp"


#' yeast tRNA gene copy numbers (GCN)
#'
#' Yeast tRNA gene copy numbers (GCN) by anticodon obtained from gtRNAdb.
#'
#' @format a named vector with a length of 41. Value names are anticodons.
#' @source <http://gtrnadb.ucsc.edu/genomes/eukaryota/Scere3/sacCer3-mature-tRNAs.fa>
#' @references Chan PP, Lowe TM. 2016. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res 44:D184-189.
#' @examples
#' yeast_trna_gcn
"yeast_trna_gcn"


#' yeast tRNA sequences
#'
#' Yeast tRNA sequences obtained from gtRNAdb.
#'
#' @format a RNAStringSet with a length of 275.
#' @source <http://gtrnadb.ucsc.edu/genomes/eukaryota/Scere3/sacCer3-mature-tRNAs.fa>
#' @references Chan PP, Lowe TM. 2016. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res 44:D184-189.
#' @examples
#' yeast_trna
"yeast_trna"


#' amino acids to codons
#'
#'  A data.frame of mapping from amino acids to codons
#'
#' @format a data.frame with two columns: amino_acid, and codon.
#' \describe{
#' \item{amino_acid}{amino acid corresponding to the codon}
#' \item{codon}{codon identity}
#' }
#' @source It is actually the standard genetic code.
#' @examples
#' aa2codon
#'
"aa2codon"