runReport {RCAS} | R Documentation |
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.
runReport( queryFilePath = "testdata", gffFilePath = "testdata", annotationSummary = TRUE, goAnalysis = TRUE, motifAnalysis = TRUE, genomeVersion = "hg19", outDir = getwd(), printProcessedTables = FALSE, sampleN = 0, quiet = FALSE, selfContained = TRUE )
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) |
An html generated using rmarkdown/knitr/pandoc that contains interactive figures, tables, and text that provide an overview of the experiment
#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)