Intro

Make omics data analysis flow :-).

Install

install.packages('remotes')
remotes::install_github('bhagwataditya/autonomics/autonomics.data',       repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.support',    repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.annotate',   repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.import',     repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.preprocess', repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.plot',       repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.find',       repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.ora',        repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics.integrate',  repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)
remotes::install_github('bhagwataditya/autonomics/autonomics',            repos = BiocManager::repositories(), dependencies = TRUE, upgrade = FALSE)

Read and prepare

# METABOLON
      require(magrittr)
      (object <- 'extdata/glutaminase/glutaminase.xlsx'    %>% 
                  system.file(package = 'autonomics.data') %>% 
                  autonomics::read_metabolon())
      object %<>% autonomics::prepare_metabolon()

# SOMASCAN
      (object <- 'extdata/stemcomp/soma/stemcomp.adat'     %>% 
                  system.file(package = 'autonomics.data') %>% 
                  autonomics::read_somascan())
      object %<>% autonomics::prepare_somascan()

# RNASEQ COUNTS
      object <- 'extdata/stemdiff/rnaseq/gene_counts.txt' %>% 
                 system.file(package = 'autonomics.data') %>% 
                 autonomics::read_counts(fid_var = 'gene_id')
      (object %<>% autonomics::prepare_rnaseq())

# RNASEQ BAMFILES

     # Download example BAM files
       url <- "https://bitbucket.org/graumannlab/billing.stemcells/downloads/stemcomp.bamfiles.zip"
       dir.create('~/.autonomics', showWarnings = FALSE)
       destfile <- "~/.autonomics/stemcomp.bamfiles.zip"
       download.file(url, destfile = destfile, )
       utils::unzip(destfile, exdir = '~/.autonomics')
       unlink(destfile)

     # Download GTF file
       gtffile <- autonomics::download_gtf('Homo sapiens', 95)

     # Read BAM files into SummarizedExperiment
       object <- autonomics::read_bam(bamdir    = "~/.autonomics/stemcomp.bamfiles",
                                      gtffile   = gtffile,
                                      ispaired  = TRUE)
     # Prepare for analysis
       object %<>% autonomics::prepare_rnaseq()


# PROTEINGROUPS
      object <- 'extdata/stemcomp/maxquant/proteinGroups.txt' %>% 
                 system.file(package = 'autonomics.data') %>% 
                 autonomics::read_proteingroups()
      object %<>% autonomics::prepare_proteingroups()

# EXIQON
      object <-  autonomics::read_exiqon(myfile)
      object %<>% autonomics::prepare_exiqon()


# ANY OMICS DATASET
      object <- 'extdata/glutaminase/glutaminase.xlsx'   %>% 
                 system.file(package = 'autonomics.data') %>% 
                 autonomics::read_omics(
                    sheet      = 2,
                    fid_rows   = 11:401,    fid_cols   = 5,
                    sid_rows   = 3,         sid_cols   = 15:86,
                    expr_rows  = 11:401,    expr_cols  = 15:86,
                    fvar_rows  = 10,        fvar_cols  = 1:14,
                    svar_rows  = 1:10,      svar_cols  = 14,
                    fdata_rows = 11:401,    fdata_cols = 1:14,
                    sdata_rows = 1:10,      sdata_cols = 15:86,
                    transpose  = FALSE)

Explore

# Sample densities
    object <- autonomics.data::glutaminase
    object %>% autonomics::plot_sample_densities(color = subgroup, facet = subgroup)
    object %>% autonomics::plot_sample_boxplots( fill  = subgroup, coord_flip = FALSE)
    object %>% autonomics::plot_sample_violins(fill  = subgroup, coord_flip = FALSE)

# Principal Component Analysis
    object <- autonomics.data::glutaminase
    object %>% autonomics::plot_pca_samples()
    object %>% autonomics::plot_pca_features()
    object %>% autonomics::plot_pca_samples_and_features(n=4)
    
#  Linear Discriminant Analysis
    object %>% autonomics::plot_lda_samples()
    object %>% autonomics::plot_lda_features()
    object %>% autonomics::plot_lda_samples_and_features()
    
# Partial Least Squares Analysis
    object %>% autonomics::plot_pls_samples()
    object %>% autonomics::plot_pls_features()
    object %>% autonomics::plot_pls_samples_and_features()

# Spectral Map Analysis
    object %>% autonomics::plot_sma_samples()          
    object %>% autonomics::plot_sma_features() 
    object %>% autonomics::plot_sma_samples_and_features()

Contrast

# Add limma
   object <- autonomics.data::glutaminase
   table(object$subgroup)
   ctrdefs <- c(uM05.h10 = 'uM05_h10 - Veh_h10', 
                uM10.h10 = 'uM10_h10 - Veh_h10')
   autonomics::contrastdefs(object) <- ctrdefs
   object %<>% autonomics::add_limma()

# Plot contrast features
   object %>% autonomics::plot_contrast_features(contrast = ctrdefs[1], n=2)
   object %>% autonomics::plot_contrast_features(contrast = ctrdefs[2], n=2)

# Write to file
   (file <- tempdir() %>% file.path('/glutaminase_results.txt'))
   object %>% autonomics::write_features(file)

# Plot volcano
   object %>% autonomics::plot_volcano()

# Plot venns
   object %>% autonomics::plot_contrast_venns(euler = TRUE)