README.md

mitocarta

This package contains the mitocarta dataset. It accompanies a workshop-style class that provides an introduction to the emerging field of Data Science in R, including data analysis and visualization, with a particular focus on its utility for biological insight. This package also contains some utility functions for simple analyses.

Installation

You cannot yet install the released version of tidybiology from CRAN with:

install.packages("mitocarta")

So in the meantime, use the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("hirscheylab/mitocarta")

Example

This is how to take a glimpse into the mitocarta dataset:

library(mitocarta)
glimpse(mitocarta)
#> Observations: 19,244
#> Variables: 43
#> $ training_dataset                          <chr> "Tnon_mito", "Tnon_mit…
#> $ human_gene_id                             <dbl> 1, 2, 9, 10, 12, 13, 1…
#> $ mouse_ortholog_gene_id                    <dbl> 117586, 232345, 17961,…
#> $ symbol                                    <chr> "A1BG", "A2M", "NAT1",…
#> $ synonyms                                  <chr> "A1B|ABG|GAB|HYST2477|…
#> $ description                               <chr> "alpha-1-B glycoprotei…
#> $ ensembl_gene_id                           <chr> "ENSG00000121410", "EN…
#> $ protein_length                            <dbl> 495, 1474, 352, 290, 4…
#> $ target_p_score                            <dbl> NA, NA, NA, NA, NA, NA…
#> $ mito_domain_score                         <chr> NA, "NonMitoDomain", "…
#> $ coexpression_gnf_n50_score                <dbl> NA, 0, 4, NA, 1, 7, 3,…
#> $ pgc_induction_score                       <dbl> NA, NA, -0.28, NA, NA,…
#> $ yeast_mito_homolog_score                  <chr> "NoMitoHomolog", "NoMi…
#> $ rickettsia_homolog_score                  <chr> "NoHomolog", "NoHomolo…
#> $ msms_score                                <chr> "50-75ambig", "50-75am…
#> $ mcarta2_score                             <dbl> -1.4533, -4.0790, -10.…
#> $ mcarta2_fdr                               <dbl> 0.459, 0.679, 0.883, 0…
#> $ mcarta2_list                              <dbl> 0, 0, 0, 0, 0, 0, 0, 0…
#> $ mcarta2_evidence                          <chr> NA, NA, NA, NA, NA, NA…
#> $ hg19_chromosome                           <chr> "chr19", "chr12", "chr…
#> $ hg19_start                                <dbl> 58858171, 9220303, 180…
#> $ hg19_stop                                 <dbl> 58864865, 9268558, 180…
#> $ msms_num_tissues                          <dbl> 1, 1, NA, NA, NA, 1, N…
#> $ msms_num_peptides_unique                  <dbl> 24, 67, NA, NA, NA, 9,…
#> $ msms_num_spectra                          <dbl> 153, 326, NA, NA, NA, …
#> $ msms_total_intensity                      <dbl> 8.11e+09, 6.93e+09, NA…
#> $ msms_percent_coverage                     <dbl> 60, 55, NA, NA, NA, 33…
#> $ tissues                                   <chr> "placenta", "placenta"…
#> $ cerebrum_total_peak_intensity_log10       <dbl> NA, NA, NA, NA, NA, NA…
#> $ cerebellum_total_peak_intensity_log10     <dbl> NA, NA, NA, NA, NA, NA…
#> $ brainstem_total_peak_intensity_log10      <dbl> NA, NA, NA, NA, NA, NA…
#> $ spinalcord_total_peak_intensity_log10     <dbl> NA, NA, NA, NA, NA, NA…
#> $ kidney_total_peak_intensity_log10         <dbl> NA, NA, NA, NA, NA, NA…
#> $ liver_total_peak_intensity_log10          <dbl> NA, NA, NA, NA, NA, 8.…
#> $ heart_total_peak_intensity_log10          <dbl> NA, NA, NA, NA, NA, NA…
#> $ skeletalmuscle_total_peak_intensity_log10 <dbl> NA, NA, NA, NA, NA, NA…
#> $ adipose_total_peak_intensity_log10        <dbl> NA, NA, NA, NA, NA, NA…
#> $ smallintestine_total_peak_intensity_log10 <dbl> NA, NA, NA, NA, NA, NA…
#> $ largeintestine_total_peak_intensity_log10 <dbl> NA, NA, NA, NA, NA, NA…
#> $ stomach_total_peak_intensity_log10        <dbl> NA, NA, NA, NA, NA, NA…
#> $ placenta_total_peak_intensity_log10       <dbl> 9.9, 9.8, NA, NA, NA, …
#> $ testis_total_peak_intensity_log10         <dbl> NA, NA, NA, NA, NA, NA…
#> $ hpa_primary_subcellular_localization_2015 <chr> NA, "Nucleus (APE, Unc…