tileCount {NADfinder} | R Documentation

## 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)
    }

[Package NADfinder version 1.18.0 Index]