createDB: createDB

In BIMSBbioinfo/RCAS: RNA Centric Annotation System

createDB

Description

Creates an sqlite database consisting of various tables of data obtained from processed BED files

Usage

createDB(
  dbPath = file.path(getwd(), "rcasDB.sqlite"),
  projDataFile,
  gtfFilePath = "",
  update = FALSE,
  genomeVersion,
  annotationSummary = TRUE,
  coverageProfiles = TRUE,
  motifAnalysis = TRUE,
  nodeN = 1
)

Arguments

dbPath	Path to the sqlite database file (could be an existing file or a new file path to be created at the given path)
projDataFile	A file consisting of meta-data about the input samples. Must minimally consist of two columns: 1. sampleName (name of the sample) 2. bedFilePath (full path to the location of the BED file containing data for the sample)
gtfFilePath	Path to the GTF file (preferably downloaded from the Ensembl database) that contains genome annotations
update	TRUE/FALSE (default: FALSE) whether an existing database should be updated
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).
annotationSummary	TRUE/FALSE (default:TRUE) whether annotation summary module should be run
coverageProfiles	TRUE/FALSE (default: TRUE) whether coverage profiles module should be run
motifAnalysis	TRUE/FALSE (default: TRUE) whether motif discovery module should be run
nodeN	Number of cpus to use for parallel processing (default: 1)

Value

Path to an SQLiteConnection object created by RSQLite package

Examples

FUS_path <- system.file("extdata", "FUS_Nakaya2013c_hg19.bed",
package='RCAS') 

FMR1_path <- system.file("extdata",
"FMR1_Ascano2012a_hg19.bed", package='RCAS') 

projData <- data.frame('sampleName' = c('FUS', 'FMR1'), 
'bedFilePath' = c(FUS_path,FMR1_path), stringsAsFactors = FALSE)
 
write.table(projData, 'myProjDataFile.tsv', sep = '\t', quote =FALSE, 
row.names = FALSE) 

gtfFilePath <- system.file("extdata",
"hg19.sample.gtf", package='RCAS')

createDB(dbPath = 'hg19.RCASDB.sqlite', 
projDataFile = './myProjDataFile.tsv', 
gtfFilePath = gtfFilePath,  
genomeVersion = 'hg19', 
motifAnalysis = FALSE, 
coverageProfiles = FALSE)

#Note: to add new data to an existing database, set update = TRUE

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