setup_sqlitedb {InPAS} | R Documentation

## Create an SQLite database for storing metadata and paths to coverage files

### Description

Create an SQLite database with five tables, "metadata","sample_coverage", "chromosome_coverage", "CPsites", and "utr3_coverage", for storing metadata (sample tag, condition, paths to bedgraph files, and sample total read coverage), sample-then-chromosome-oriented coverage files (sample tag, chromosome, paths to bedgraph files for each chromosome), and paths to chromosome-then-sample-oriented coverage files (chromosome, paths to bedgraph files for each chromosome), CP sites on each chromosome (chromosome, paths to cpsite files), read coverage for 3' UTR and last CDS regions on each chromosome (chromosome, paths to utr3 coverage file), respectively

### Usage

    setup_sqlitedb(metadata, outdir)

### Arguments

`metadata` | A path to a tab-delimited file, with columns "tag", "condition", and "bedgraph_file", storing a unique name tag for each sample, a condition name for each sample, such as "treatment" and "control", and a path to the bedgraph file for each sample
`outdir` | A character(1) vector, a path with write permission for storing the SQLite database. If it doesn't exist, it will be created.

### Value

A character(1) vector, the path to the SQLite database

### Author(s)

Haibo Liu

### Examples

    if (interactive()) {
       bedgraphs <- system.file("extdata",c("Baf3.extract.bedgraph",
                                            "UM15.extract.bedgraph"),
                               package = "InPAS")
       tags <- c("Baf3", "UM15")
       metadata <- data.frame(tag = tags,
                              condition = c("Baf3", "UM15"),
                              bedgraph_file = bedgraphs)
       outdir = tempdir()
       write.table(metadata, file =file.path(outdir, "metadata.txt"),
                   sep = "\t", quote = FALSE, row.names = FALSE)
       sqlite_db <- setup_sqlitedb(metadata =
                                     file.path(outdir, "metadata.txt"),
                                   outdir)
    }

[Package InPAS version 2.2.0 Index]