runReport: Generate a RCAS Report for a list of transcriptome-level...

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

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)

BIMSBbioinfo/RCAS documentation built on Feb. 7, 2024, 4:38 p.m.