get_chromosomes: Identify chromosomes/scaffolds for CP site discovery

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

Identify chromosomes/scaffolds for CP site discovery

Description

Identify chromosomes/scaffolds which have both coverage and annotated 3' utr3 for CP site discovery

Usage

get_chromosomes(utr3, sqlite_db)

Arguments

utr3	An object of GenomicRanges::GRangesList. An output of extract_UTR3Anno().
sqlite_db	A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb().

Value

A vector of characters, containing names of chromosomes/scaffolds for CP site discovery

Examples

library(BSgenome.Mmusculus.UCSC.mm10)
genome <- BSgenome.Mmusculus.UCSC.mm10
data(utr3.mm10)
utr3 <- split(utr3.mm10, seqnames(utr3.mm10), drop = TRUE)
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
)
addLockName(filename = tempfile())
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,
      chr2exclude = "chrM"
    )
}
get_chromosomes(utr3, sqlite_db)

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