estFragmentLength {ChIPpeakAnno} | R Documentation

## 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))
            }
        }

[Package ChIPpeakAnno version 3.24.2 Index]