runReportMetaAnalysis: runReportMetaAnalysis

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

runReportMetaAnalysis

Description

Generate a stand-alone HTML report with interactive figures and tables from a pre-calculated RCAS database (using RCAS::createDB) to compare multiple samples.

Usage

runReportMetaAnalysis(
  dbPath = "RCAS.sqlite",
  sampleTablePath,
  outDir = getwd(),
  outFile = NULL,
  quiet = FALSE,
  selfContained = TRUE
)

Arguments

dbPath	Path to the sqlite database generated by RCAS::createDB
sampleTablePath	A tab-separated file with two columns (no rownames) header 1: sampleName, header 2: sampleGroup
outDir	Path to the output directory. (default: current working directory)
outFile	Name of the output HTML report (by default, the base name of sampleTablePath value is used to create a name for the HTML report)
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

dbPath <- system.file("extdata", "hg19.RCASDB.sqlite",
package='RCAS') 

#Hint: use RCAS::summarizeDatabaseContent to see which samples have processed
#data in the database. 
summarizeDatabaseContent(dbPath = dbPath)

#Create a data table for samples and their groups sampleGroup field is used
#to group replicates of #the same sample into one group in visualizations. 
#Any arbitrary name can be used for sampleGroup field. However, entries in
#the sampleName field must be available in the queried database
sampleData <- data.frame('sampleName' = c('FUS', 'FMR1'), 
    'sampleGroup' = c('FUS', 'FMR1'), stringsAsFactors = FALSE) 
write.table(sampleData, 'sampleDataTable.tsv', sep = '\t', 
    quote =FALSE, row.names = FALSE)
#Use the generated database to run a report 
runReportMetaAnalysis(dbPath = 'hg19.RCASDB.sqlite', 
    sampleTablePath = 'sampleDataTable.tsv')

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