View source: R/04.get_chromosomes.R
get_chromosomes | R Documentation |
Identify chromosomes/scaffolds which have both coverage and annotated 3' utr3 for CP site discovery
get_chromosomes(utr3, sqlite_db)
utr3 |
An object of GenomicRanges::GRangesList. An output of
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sqlite_db |
A path to the SQLite database for InPAS, i.e. the output of
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A vector of characters, containing names of chromosomes/scaffolds for CP site discovery
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)
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