tileCount: Perform overlap queries between reads and genome by windows

In jianhong/NADfinder: Call wide peaks for sequencing data

Perform overlap queries between reads and genome by windows

Description

tileCount extends summarizeOverlaps by finding coverage for each fixed window in the whole genome

Usage

tileCount(
  reads,
  genome,
  excludeChrs = c("chrM", "M", "Mt", "MT"),
  windowSize = 50000,
  step = 10000,
  mode = IntersectionNotStrict,
  dataOverSamples = FALSE,
  ...
)

Arguments

reads	A GRanges, GRangesList (should be one read per list element), GAlignments, GAlignmentsList, GAlignmentPairs or BamFileList object that represents the data to be counted by summarizeOverlaps. If reads are more than 1 bam files, it should be a vector of character with full path, otherwise current working directory is the default directory.
genome	A BSgenome object from/on which to get/set the sequence and metadata information.
excludeChrs	A vector of string: chromosomes/scaffolds of no interest for NAD analysis. see summarizeOverlaps. default is countByOverlaps, alia of countOverlaps(features, reads, ignore.strand=ignore.strand)
windowSize	numeric(1) or integer(1). Size of the windows.
step	numeric(1) or integer(1). Step of generating silding windows.
mode	One of the pre-defined count methods.
dataOverSamples	logical(1). Data over several samples when use GRangesList as input.
...	Additional arguments passed to summarizeOverlaps.

Value

A RangedSummarizedExperiment object. The assays slot holds the counts, rowRanges holds the annotation from the sliding widows of genome. metadata contains lib.size.chrom for holding chromosome-level sequence depth

Author(s)

Jianhong Ou, Haibo Liu, Herve Pages and Julie Zhu

Examples

if (interactive())
{
    fls <- list.files(system.file("extdata", package="NADfinder"),
    recursive=FALSE, pattern="*bam$", full=TRUE)
    names(fls) <- basename(fls)
    if (!require(BSgenome.Mmusculus.UCSC.mm10))
    {
        if (!requireNamespace("BiocManager", quietly=TRUE))
        install.packages("BiocManager")
        BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")
        library(BSgenome.Mmusculus.UCSC.mm10)
    }
    se <- tileCount(reads = fls, 
                    genome = Mmusculus,
                    excludeChrs = c("chrM", paste0("chr", c(1:17,19)), 
                                    "chrX", "chrY"), 
                    windowSize=50000, step=10000)
}

jianhong/NADfinder documentation built on Oct. 29, 2023, 11:08 a.m.