tileCount2 {NADfinder} | R Documentation

## Perform overlap queries between reads and genome by sliding windows Count reads over sliding windows.

### Description

Perform overlap queries between reads and genome by sliding windows Count reads over sliding windows.

if (interactive()) fls <- list.files(system.file("extdata", package="NADfinder"), recursive=FALSE, pattern="*bam$", full=TRUE) names(fls) <- basename(fls)

se <- tileCount2(reads = fls, windowSize=50000, step=10000)

### Usage

    tileCount2(
      reads,
      fragment.length = 100,
      windowSize = 50000,
      restrict = paste0("chr", c(1:19, "X", "Y")),
      step = 1000,
      filter = 0,
      pe = "both"
    )

    tileCount2(
      reads,
      fragment.length = 100,
      windowSize = 50000,
      restrict = paste0("chr", c(1:19, "X", "Y")),
      step = 1000,
      filter = 0,
      pe = "both"
    )

### Arguments

`reads` | An object that represents the names and path of the bam files to be counted. If reads are more than 1 bam files, it should be a vector of character with full path. This function now works for paired end reads
`fragment.length` | integer(1). An integer scalar or a list of two integer scalars/vectors, containing the average length(s) of the sequenced fragments in each libary.
`windowSize` | numeric(1) or integer(1). Size of the windows.
`restrict` | restrict to a set of chromosomes, default to mouse chromosomes.
`step` | numeric(1) or integer(1). Step of generating silding windows.
`filter` | default to 0 without filtering. An integer scalar for the minimum count sum across libraries for each window
`pe` | a character string indicating whether paired-end data is present; set to "none", "both", "first" or "second"

### Value

A RangedSummarizedExperiment object with chromosome-level depth 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)

Jun Yu,Hervé Pagès and Julie Zhu

### Examples

    if (interactive())
    {
        fls <- list.files(system.file("extdata", package="NADfinder"),
        recursive=FALSE, pattern="*bam$", full=TRUE)
        names(fls) <- basename(fls)

        se <- tileCount2(reads = fls,
                        windowSize=50000, step=10000)
    }

[Package NADfinder version 1.12.0 Index]