csaw (version 1.4.0)

makeExtVector: Make an extVector object

Description

Construct an extVector to hold read extension parameters.

Usage

makeExtVector(ext, final.ext=NULL)

Arguments

ext

an integer scalar or vector containing average fragment lengths for read extension in one or more libraries

final.ext

an integer scalar, specifying the length to which all fragments are scaled

Value

An extVector object containing the values of ext, with the value of final.ext stored in the attributes.

Details

This function returns an extVector object, which is just an augmented integer vector with the final.ext attribute. The aim of using a specialized class is to preserve attributes during subsetting. Thus, functions like windowCounts or regionCounts can be run with different combinations of libraries, and final.ext will be maintained in each call.

The values in ext will ultimately be used for directional extension, to infer the fragment corresponding to each read. Different fragment lengths will be used in different libraries if a vector is supplied for ext. If final.ext is NULL, it is defined by makeExtVector as the mean of all ext.

Lengths of all fragments will be scaled to the same final.ext value in each library. If final.ext is NA, no scaling is performed. See windowCounts for more details.

See Also

windowCounts, regionCounts

Examples

out <- makeExtVector(1:5*10, NA)
out
out[1:2]

out <- makeExtVector(1:5*10, NULL)
out
out[1:2] # Doesn't recalculate, which is correct.