R/global_variables.R

In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database

#'
#' set global variables, mostly as a hack to make the tidyverse data binding pass the R CMD Check
#'
#' @import tibble
#'
database_colnames = c("bioSampleNumber","harvestDate","harvester","experimentDesign","experimentObservations",
                      "bioSampleObservations","baseStrain","strain","genotype1","perturbation1","marker1","genotype2",
                      "perturbation2", "marker2","medium","temperature","atmosphere","treatment","treatmentConc",
                      "treatmentConcUnit","otherConditions","pH","timePoint","replicate","floodmedia","inductionDelay",
                      "rnaSampleNumber","rnaDate","rnaPreparer","rnaSampleObservations","rnaPrepMethod",
                      "roboticRNAPrep","ribosomalBand","ribosomalBandShape","smallRNABands","rin",
                      "s1cDNASampleNumber","s1cDNADate","s1cDNAPreparer","s1Observations","polyAIsolationProtocol",
                      "s1cDNAProtocol","roboticS1Prep","s1PrimerSeq","s2cDNASampleNumber","s2cDNADate",
                      "s2cDNAPreparer","s2Observations","s2cDNAProtocol","roboticS2Prep","PooledSecondStrand",
                      "librarySampleNumber","libraryDate","libraryPreparer","libraryObservations","index1Sequence",
                      "libraryProtocol","index1Name","index2Name","index2Sequence","roboticLibraryPrep",
                      "fastqFileNumber","fastqFileName","fastqObservations","runNumber","purpose","laneNumber",
                      "sequencerModel","flowcellType","tapestationConc","volumePooled","readsObtained",
                      "qualityAssessmentNumber","manualAudit","manualStatus","librarySize","effectiveLibrarySize",
                      "uniqueAlignment","effectiveUniqueAlignment","effectiveUniqueAlignmentPercent","multiMap",
                      "proteinCodingTotal","proteinCodingTotalPercent","noMap","proteinCodingCounted",
                      "proteinCodingCountedPercent","homopolymerFilter","multiMapPercent","readLengthFilter",
                      "ambiguousFeaturePercent","noFeature","noFeaturePercent","ambiguous","intergenicCoverage",
                      "tooLowAqual","notAlignedTotalPercent","notAligned","noMapPercent","alignmentNotUnique",
                      "homopolyFilterPercent","readLengthFilterPercent","tooLowAqualPercent","rRnaPercent",
                      "nctrRnaPercent","autoAudit","autoStatus","autoStatusDecomp","genotype1Coverage",
                      "genotype1Log2cpm","genotype2Coverage","genotype2Log2cpm","overexpressionFOW","natCoverage",
                      "natLog2cpm","g418Coverage","g418Log2cpm","interquartileRange","totaleDeduplicatedPercentage")

# remove these when the "old qc colnames" no longer matter (after the old rnaseq_pipeline package is taken down)
old_qc_colnames = c("LIBRARY_SIZE","EFFECTIVE_LIBRARY_SIZE","EFFECTIVE_UNIQUE_ALIGNMENT",
                    "EFFECTIVE_UNIQUE_ALIGNMENT_PERCENT","MULTI_MAP_PERCENT","PROTEIN_CODING_TOTAL",
                    "PROTEIN_CODING_TOTAL_PERCENT","PROTEIN_CODING_COUNTED","PROTEIN_CODING_COUNTED_PERCENT",
                    "AMBIGUOUS_FEATURE_PERCENT","NO_FEATURE_PERCENT","INTERGENIC_COVERAGE",
                    "NOT_ALIGNED_TOTAL_PERCENT","GENOTYPE1_COVERAGE","GENOTYPE1_LOG2CPM",
                    "GENOTYPE2_COVERAGE","GENOTYPE2_LOG2CPM","OVEREXPRESSION_FOW","NAT_COVERAGE",
                    "NAT_LOG2CPM","G418_COVERAGE",'G418_LOG2CPM',"NO_MAP_PERCENT","HOMOPOLY_FILTER_PERCENT",
                    "READ_LENGTH_FILTER_PERCENT","TOO_LOW_AQUAL_PERCENT","rRNA_PERCENT","nctrRNA_PERCENT",
                    "STATUS","AUTO_AUDIT","STATUS_DECOMP", "EFFECTIVEUNIQUE_ALIGNMENT")

# TODO all global variables should be capitalized from now on -- uncapitalized variables should be made capital
misc = c("GENOTYPE", "STRAIN_STATUS", "RLE", "TOTALDEDUPLICATEDPERCENTAGE", "qc_passing_iqr_filtered",
         "qc_passing", "complete_set_no_fltr", "replicate_tally", "model_params",
         "norm_count", ".x", "quant_type", ".", "Bam_file", "fastq_1", "fastq_2", "strandedness", "quantile",
         "IQR", "Sample", "Expression\ Profiling\ Efficiency", "Exonic\ Rate", "Intronic\ Rate", "Intergenic\ Rate",
        "Intragenic\ Rate", "rRNA\ Rate", "Estimated\ Library\ Complexity", "expression_profiling_efficiency",
        "exonic_rate", "intronic_rate", "intergenic_rate", "intragenic_rate", "rRna_rate", "estimated_library_complexity",
        "V1", "V2", "destination")

# shiny_app_vars = c('actionButton', 'audit_flag', 'checkboxGroupInput', 'column', 'downloadButton',
#                    'downloadHandler', 'eventReactive', 'fluidRow', 'icon', 'metric', 'numericInput',
#                    'observeEvent', 'prepend', 'radioButtons', 'reactiveValues', 'reduce', 'req',
#                    'selectInput', 'shinyApp', 'showNotification', 'sliderInput', 'status', 'statusDecomp',
#                    'tabPanel', 'tabPanelBody', 'tabsetPanel', 'updateCheckboxGroupInput',
#                    'updateNumericInput', 'updateRadioButtons', 'updateSelectInput',
#                    'updateSliderInput', 'updateTabsetPanel')

package_data_variables = c("test_metadata", "run_numbers_with_leading_zero")

global_variables_vector = c(database_colnames, old_qc_colnames, misc,
                      package_data_variables) #shiny_app_vars

utils::globalVariables(global_variables_vector)
utils::globalVariables(toupper(global_variables_vector))