estFragmentLength: estimate the fragment length

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

estimate the fragment length

Description

estimate the fragment length for bam files

Usage

estFragmentLength(
  bamfiles,
  index = bamfiles,
  plot = TRUE,
  lag.max = 1000,
  minFragmentSize = 100,
  ...
)

Arguments

bamfiles	The file names of the 'BAM' ('SAM' for asBam) files to be processed.
index	The names of the index file of the 'BAM' file being processed; this is given without the '.bai' extension.
plot	logical. If TRUE (the default) the acf is plotted.
lag.max	maximum lag at which to calculate the acf. See acf
minFragmentSize	minimal fragment size to avoid the phantom peak.
...	Not used.

Value

numberic vector

Author(s)

Jianhong Ou

Examples

    if(interactive() || Sys.getenv("USER")=="jianhongou"){
        path <- system.file("extdata", "reads", package="MMDiffBamSubset")
        if(file.exists(path)){
            WT.AB2 <- file.path(path, "WT_2.bam")
            Null.AB2 <- file.path(path, "Null_2.bam")
            Resc.AB2 <- file.path(path, "Resc_2.bam")
            estFragmentLength(c(WT.AB2, Null.AB2, Resc.AB2))
        }
    }
    

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.