runReport {RCAS} | R Documentation

## Generate a RCAS Report for a list of transcriptome-level segments

### Description

This is the main report generation function for RCAS. This function can take a BED file, a GTF file and optionally an MSIGDB gene set annotation (or any text file containing annotations with the same structure as defined in MSIGDB); and use these input to run multiple RCAS functions to create a summary report regarding the annotation data that overlap the input BED file, enrichment analysis for GO terms, gene sets from MSIGDB, and motif analysis.

### Usage

    runReport(queryFilePath = "testdata", gffFilePath = "testdata",
      msigdbFilePath = "testdata", annotationSummary = TRUE,
      goAnalysis = TRUE, msigdbAnalysis = TRUE, motifAnalysis = TRUE,
      genomeVersion = "hg19", outDir = getwd(),
      printProcessedTables = FALSE, sampleN = 0, quiet = FALSE,
      selfContained = TRUE)

### Arguments

`queryFilePath` | a BED format file which contains genomic coordinates of protein-RNA binding sites
`gffFilePath` | A GTF format file which contains genome annotations (preferably from ENSEMBL)
`msigdbFilePath` | Gene set annotations for Homo sapiens from Molecular Signatures Database or any text file that has the same structure. Regardless of which species is being studied (see genomeVersion parameter), msigdbFilePath must contain annotations for human genes. The gene sets will be mapped from human to other species if genomeVersion is set to anything except human genome versions (e.g. mm9 or dm3).
`annotationSummary` | TRUE/FALSE (default: TRUE) A switch to decide if RCAS should provide annotation summaries from overlap operations
`goAnalysis` | TRUE/FALSE (default: TRUE) A switch to decide if RCAS should run GO term enrichment analysis
`msigdbAnalysis` | TRUE/FALSE (default: TRUE) A switch to decide if RCAS should run gene set enrichment analysis
`motifAnalysis` | TRUE/FALSE (default: TRUE) A switch to decide if RCAS should run motif analysis
`genomeVersion` | A character string to denote for which genome version the analysis is being done. Available options are hg19/hg38 (human), mm9/mm10 (mouse), ce10 (worm) and dm3 (fly).
`outDir` | Path to the output directory. (default: current working directory)
`printProcessedTables` | boolean value (default: FALSE). If set to TRUE, raw data tables that are used for plots/tables will be printed to text files.
`sampleN` | integer value (default: 0). A parameter to determine if the input query regions should be downsampled to a smaller size in order to make report generation quicker. When set to 0, downsampling won't be done. To activate the sampling a positive integer value that is smaller than the total number of query regions should be given.
`quiet` | boolean value (default: FALSE). If set to TRUE, progress bars and chunk labels will be suppressed while knitting the Rmd file.
`selfContained` | boolean value (default: TRUE). By default, the generated html file will be self-contained, which means that all figures and tables will be embedded in a single html file with no external dependencies (See rmarkdown::html_document)

### Value

An html generated using rmarkdown/knitr/pandoc that contains interactive figures, tables, and text that provide an overview of the experiment

### Examples

    #Default run will generate a report using built-in test data for hg19 genome.
    ## Not run:
    runReport()

    ## End(Not run)

    #A custom run for human
    ## Not run:
    runReport( queryFilePath = 'input.BED',
               gffFilePath = 'annotation.gtf',
               msigdbFilePath = 'human_msigdb.gmt')

    ## End(Not run)
    # To turn off certain modules of the report
    ## Not run:
    runReport( queryFilePath = 'input.BED',
               gffFilePath = 'annotation.gtf',
               msigdbFilePath = 'human_msigdb.gmt',
               motifAnalysis = FALSE,
               goAnalysis = FALSE )

    ## End(Not run)
    # To run the pipeline for species other than human
    # If the msigdb module is needed, the msigdbFilePath
    # must be set to the MSIGDB annotations for 'human'.
    # MSIGDB datasets for other species will be calculated
    # in the background using the createOrthologousMsigdbDataset
    # function
    ## Not run:
    runReport( queryFilePath = 'input.mm9.BED',
               gffFilePath = 'annotation.mm9.gtf',
               msigdbFilePath = 'msigdb.human.gmt',
               genomeVersion = 'mm9' )

    ## End(Not run)

[Package RCAS version 1.12.0 Index]