| 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)
}