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 takes a BED file, a GTF file to create a summary report regarding the annotation data that overlap the input BED file, enrichment analysis for functional terms, and motif analysis.

### Usage

    runReport(
      queryFilePath = "testdata",
      gffFilePath = "testdata",
      annotationSummary = TRUE,
      goAnalysis = 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)
`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
`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.
`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',
               genomeVersion = 'hg19')

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

    ## End(Not run)

[Package RCAS version 1.14.0 Index]