get_usage4plot {InPAS} | R Documentation |
prepare coverage data and fitting data for plot
get_usage4plot(gr, proximalSites, sqlite_db, hugeData)
gr |
an object of GenomicRanges::GRanges |
proximalSites |
An integer(n) vector, specifying the coordinates of
proximal CP sites. Each of the proximal sites must match one entry in the
GRanges object, |
sqlite_db |
A path to the SQLite database for InPAS, i.e. the output of
|
hugeData |
A logical(1), indicating whether it is huge data |
An object of GenomicRanges::GRanges with metadata:
dat |
A data.frame, first column is the position, the other columns are Coverage and value |
offset |
offset from the start of 3' UTR |
Jianhong Ou, Haibo Liu
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("baf", "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 = TRUE) data4CPsSearch <- setup_CPsSearch(sqlite_db, genome, utr3, background = "10K", TxDb = TxDb, removeScaffolds = TRUE, BPPARAM = NULL, hugeData = TRUE, outdir = outdir) gr <- GRanges("chr6", IRanges(128846245, 128850081), strand = "-") names(gr) <- "chr6:128846245-128850081" data4plot <- get_usage4plot(gr, proximalSites = 128849148, sqlite_db, hugeData = TRUE) plot_utr3Usage(usage_data = data4plot, vline_color = "purple", vline_type = "dashed")