assemble_allCov {InPAS}R Documentation

Assemble coverage files 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, outdir, genome, removeScaffolds = FALSE)

Arguments

sqlite_db

A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb()

outdir

A character(1) vector, a path with write permission for storing the coverage data. If it doesn't exist, it will be created.

genome

An object of BSgenome::BSgenome

removeScaffolds

A logical(1) vector, whether the scaffolds should be removed from the genome If you use a TxDb containing alternative scaffolds, you'd better to remove the scaffolds.

Value

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

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()
   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,
                            removeScaffolds = TRUE,
                            BPPARAM = NULL)
   }
   coverage_files <- assemble_allCov(sqlite_db, 
                                    outdir, 
                                    genome, 
                                    removeScaffolds = FALSE)
}

[Package InPAS version 2.1.0 Index]