setup_sqlitedb: Create an SQLite database for storing metadata and paths to...

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

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 = getInPASOutputDirectory())

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 InPAS analysis results. 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
  )
}

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.