tileCount2: Perform overlap queries between reads and genome by sliding...

In jianhong/NADfinder: Call wide peaks for sequencing data

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)
}

jianhong/NADfinder documentation built on May 9, 2024, 2:22 p.m.