assemble_allCov: Assemble coverage files for a given chromosome for all...

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

Assemble coverage files for a given chromosome for all samples

Description

Process individual sample-chromosome-specific coverage files in an experiment into a file containing a list of chromosome-specific Rle coverage of all samples

Usage

assemble_allCov(
  sqlite_db,
  seqname,
  outdir = getInPASOutputDirectory(),
  genome = getInPASGenome()
)

Arguments

sqlite_db	A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb()
seqname	A character(1) vector, the name of a chromosome/scaffold
outdir	A character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created.
genome	An object of BSgenome::BSgenome

Value

A list of paths to per-chromosome coverage files of all samples.

• seqname, chromosome/scaffold name

  • tag1, name tag for sample1

  • tag2, name tag for sample2

  • tagN, name tag for sampleN

Author(s)

Haibo Liu

Examples

if (interactive()) {
  library(BSgenome.Mmusculus.UCSC.mm10)
  genome <- BSgenome.Mmusculus.UCSC.mm10
  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
  )
  coverage <- list()
  addLockName(filename = tempfile())
  for (i in seq_along(bedgraphs)) {
    coverage[[tags[i]]] <- get_ssRleCov(
      bedgraph = bedgraphs[i],
      tag = tags[i],
      genome = genome,
      sqlite_db = sqlite_db,
      outdir = outdir,
      chr2exclude = "chrM"
    )
  }
  chr_coverage <- assemble_allCov(sqlite_db,
    seqname = "chr6",
    outdir = outdir,
    genome = genome
  )
}

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