getWidths: Get region widths

In LTLA/csaw: ChIP-Seq Analysis with Windows

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)

LTLA/csaw documentation built on Dec. 11, 2023, 5:11 a.m.