setup_CPsSearch {InPAS} | R Documentation

## prepare data for predicting cleavage and polyadenylation (CP) sites

### Description

prepare data for predicting cleavage and polyadenylation (CP) sites

### Usage

    setup_CPsSearch(
      sqlite_db,
      genome,
      utr3,
      background = c("same_as_long_coverage_threshold", "1K", "5K", "10K", "50K"),
      TxDb = NA,
      removeScaffolds = FALSE,
      hugeData = TRUE,
      outdir,
      BPPARAM = NULL,
      silence = FALSE
    )

### Arguments

`sqlite_db` | A path to the SQLite database for InPAS, i.e. the output of `setup_sqlitedb()`.
`genome` | An object of BSgenome::BSgenome
`utr3` | An object of GenomicRanges::GRangesList, output of `extract_UTR3Anno()`
`background` | A character(1) vector, the range for calculating cutoff threshold of local background. It can be "same_as_long_coverage_threshold", "1K", "5K","10K", or "50K".
`TxDb` | an object of GenomicFeatures::TxDb
`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.
`hugeData` | A logical(1) vector, indicating whether it is huge data
`outdir` | A character(1) vector, a path with write permission for storing the coverage data. If it doesn't exist, it will be created.
`BPPARAM` | an optional BiocParallel::BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to bplapply. It can be set to NULL or bpparam()
`silence` | report progress or not. By default it doesn't report progress.

### Value

A list as described below:

utr3TotalCov

  chromosome-wise 3' UTR coverage in summarized View format

chr1

  A filename for chr1 3' UTR coverage in summarized View format

chr2

  A filename for chr2 3' UTR coverage in summarized View format

chrN

  A filename for chrN 3' UTR coverage in summarized View format

background

  The type of methods for bckground coverage calculation

z2s

  Z-score cutoff thresholds for each 3' UTRs

depth.weight

  A named vector containing depth weight

### Author(s)

Jianhong Ou, Haibo Liu

@examples if (interactive()) library(BSgenome.Mmusculus.UCSC.mm10) library("TxDb.Mmusculus.UCSC.mm10.knownGene")

    genome <- BSgenome.Mmusculus.UCSC.mm10
    TxDb <- TxDb.Mmusculus.UCSC.mm10.knownGene

    ## load UTR3 annotation and convert it into a GRangesList
    data(utr3.mm10)
    utr3 <- split(utr3.mm10, seqnames(utr3.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)
    }
    coverage_files <- assemble_allCov(sqlite_db,
                                     outdir,
                                     genome,
                                     removeScaffolds = TRUE)
    data4CPsitesSearch <- setup_CPsSearch(sqlite_db,
                                          genome,
                                          utr3,
                                         background = "10K",
                                         TxDb = TxDb,
                                         removeScaffolds = TRUE,
                                         hugeData = TRUE,
                                         outdir = outdir)

[Package InPAS version 2.2.0 Index]