getWidths {csaw} | R Documentation

## Get region widths

### Description

Get the widths of the read counting interval for each region.

### Usage

    getWidths(data)

### Arguments

`data` | a `RangedSummarizedExperiment` object, produced by `windowCounts` or `regionCounts`

### Details

Widths of all regions are increased by the average fragment length during the calculations. This is because each count represents the number of (imputed) fragments overlapping each region. Thus, a 1 bp window has an effective width that includes the average length of each fragment.

The fragment length is taken from `metadata(data)$final.ext`, if it is a valid integer. If `NULL`, it is set to 1, and if `NA`, it is taken from `data$ext`. If the fragment lengths are different between libraries, the average is used to compute the effective width of the window. For paired-end data, `data$ext` should be an average of the inferred fragment sizes, e.g., obtained with `getPESizes`.

If `final.ext` is `NA` and any of `ext` are `NA`, the function will extract the read lengths in `data$rlen`. This is because `NA` values of `ext` correspond to the use of unextended reads in `windowCounts` and `regionCounts`. The likely read lengths are automatically computed in each function but can also be set manually.

### Value

An integer vector containing the effective width, in base pairs, of each region.

### Author(s)

Aaron Lun

### See Also

`windowCounts`, `regionCounts`

### Examples

    bamFiles <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
    data <- windowCounts(bamFiles, filter=1)
    getWidths(data)

    # Average is used when multiple fragment lengths are present.
    data <- windowCounts(bamFiles, ext=list(c(50, 100), NA), filter=1)
    getWidths(data)

    # Using the automatically computed 'rlen'.
    data <- windowCounts(bamFiles, ext=NA, filter=1)
    getWidths(data)
    data$rlen <- 200 # Manually defining it, if required.
    getWidths(data)

    # Paired-end data also takes the fragment length from 'ext'.
    bamFile <- system.file("exdata", "pet.bam", package="csaw")
    data <- windowCounts(bamFile, param=readParam(pe="both"), filter=1)
    getWidths(data)
    data$ext <- 200 # Again, manual definition is accepted.
    getWidths(data)

[Package csaw version 1.26.0 Index]