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.

Usage

tileCount2(reads, 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 funciton now if for paired end reads

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

pe

a character string indicating whether paired-end data is present; set to "none", "both", "first" or "second"

Value

return a summarized experiment object with chromosome-level depth information for each input sample as metadata.

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)

Jun Yu

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 1.4.0 Index]