mitocarta: Mitocarta Data Set and Utility Functions

#' Mitocarta: an inventory of mammalian mitochondrial genes
#'
#' MitoCarta2.0 is an inventory of 1158 human genes encoding proteins with strong support of mitochondrial localization. To generate this inventory, the Mootha lab at MGH performed mass spectrometry of mitochondria isolated from fourteen tissues, assessed protein localization through large-scale GFP tagging/microscopy, and integrated these results with six other genome-scale datasets of mitochondrial localization, using a Bayesian approach. MitoCarta2.0, released 2015, is an update from the MitoCarta1.0 inventory published in Cell, 2008.
#'
#' @usage data(mitocarta)
#'
#' @docType data
#'
#' @format A data frame with 19,244 rows and 43 variables:
#' \describe{
#'   \item{training_dataset}{Tmito, Tnot_mito, or T_possible_mito (indicating evidence based on NCBI GO mitochondrial annotation or MitoP2 database, but not in Tmito)}
#'   \item{human_gene_id}{NCBI Entrez Gene ID for human ortholog of mouse gene (based on reciprocal BLASTP hit, expect<1e-3)}
#'   \item{mouse_ortholog_gene_id}{NCBI Entrez Gene ID for mouse gene}
#'   \item{symbol}{Official Entrez gene symbol}
#'   \item{synonyms}{NCBI Entrez gene synonyms (UniProt added at end)}
#'   \item{description}{NCBI Entrez gene description}
#'   \item{ensembl_gene_id}{Ensembl Gene Identifier (based on Ensembl mapper)}
#'   \item{protein_length}{Length of longest RefSeq protein isoform}
#'   \item{target_p_score}{TargetP confidence score (1-5, 1 is most confident) of mitochondrial targeting signal. Score 0 indicates no mitochondrial prediction}
#'   \item{mito_domain_score}{MitoDomain indicates exclusively mito domain; SharedDomain indicates shared mito & non-mito domain; NonMitoDomain indicates exclusively non-mito domain; NA indicates unknown}
#'   \item{coexpression_gnf_n50_score}{N50 score for coexpression across mouse GNFv3 tissue atlas (N50 = number of 50 nearest neighbors that are in Tmito)}
#'   \item{pgc_induction_score}{Foldchange in transcript induction following overexpression of PGC1a, known to induce mitochondrial biogenesis}
#'   \item{yeast_mito_homolog_score}{OrthologMitoHighConf (HomologMitoHighConf) if yeast ortholog (homolog) is annotated mitochondrial in SGD with high confidence; OrthologMitoLowConf (HomologMitoLowConf) if yeast ortholog (homolog) is annotated mitochondrial in SGD with low confidence (dual localized or only based on high throughput data), NoMitoHomolog indicates no yeast homolog or homolog is not annotated mitochondrial in SGD}
#'   \item{rickettsia_homolog_score}{Ortholog if 1:1 ortholog between mouse and Rickettsia prowazekii; Homolog if homology between mouse and Rickettsia prowazekii, otherwise NoHomolog}
#'   \item{msms_score}{Category indicating MS/MS abundance (coverage) and enrichment in subtractive proteomics (either pure-enriched, crude-enriched, or ambiguous)}
#'   \item{mcarta2_score}{Naïve Bayes score (sum of log-likelihood ratios for each of 7 above features)}
#'   \item{mcarta2_fdr}{Estimated corrected false discovery rate for all predictions >= given score}
#'   \item{mcarta2_list}{1 if gene is on final MitoCarta2.0 list}
#'   \item{mcarta2_evidence}{Type of experimental support}
#'   \item{hg19_chromosome}{Chromosome (hg19 assembly)}
#'   \item{hg19_start}{Start position (hg19)}
#'   \item{hg19_stop}{Stop position (hg19)}
#'   \item{msms_num_tissues}{Number 0-14 tissues where gene products were found by MS/MS }
#'   \item{msms_num_peptides_unique}{Number of unique peptides, based on pooling spectra from 14 tissues}
#'   \item{msms_num_spectra}{Number of spectra corresponding to this gene, based on pooling spectra from 14 tissues}
#'   \item{msms_total_intensity    }{total peak intensity, based on pooling spectra from 14 tissues}
#'   \item{msms_percent_coverage}{Coverage (percent of amino acids covered by MS/MS spectra), based on pooling spectra from 14 tissues}
#'   \item{tissues}{List of tissues with evidence of protein, based on 14 tissues}
#'   \item{cerebrum_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{cerebellum_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{brainstem_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{spinalcord_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{kidney_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{liver_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{heart_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{skeletalmuscle_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{adipose_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{smallintestine_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{largeintestine_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{stomach_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{placenta_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{testis_total_peak_intensity_log10}{Total peak intensity of spectra found in this tissue (log base 10)}
#'   \item{hpa_primary_subcellular_localization_2015}{Human Protein Atlas [September 2015] designation of primary subcellular localization based on immunofluorescence of antibodies in 3 human cell lines; Text in parenthesis indicates antibody reliability (where APE=antibody protein expression)}
#' }
#'
#' @keywords datasets
#'
#' @source \url{https://www.broadinstitute.org/scientific-community/science/programs/metabolic-disease-program/publications/mitocarta/mitocarta-in-0}
"mitocarta"