assemble_allCov {InPAS} | R Documentation |
Process individual sample-chromosome-specific coverage files in an experiment into a file containing a list of chromosome-specific Rle coverage of all samples
assemble_allCov(sqlite_db, outdir, genome, removeScaffolds = FALSE)
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. |
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
Haibo Liu
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) }