subtract-functions: Subtract functions

In TSSi: Transcription Start Site Identification

Description

Functions subtracting the expectation value used in the identification of TSS.

Usage

subtractExpectation(fg, bg, indTss, pos, basal, tau, extend=FALSE)

Arguments

fg	Numeric vector with foreground.
bg	Numeric vector with background of the same length as fg.
indTss	Index vector indicating the expected TSS sites in fg.
pos	Positions of the reads in the segment, as given in the segmentizeCounts method.
basal	See the normalizeCounts method.
tau	See the identifyStartSites method.
extend	Logical indicating whether the background estimates should be computed for all positions, rather than only for those with reads.

Details

The subtractExpectation function is one approach on how to subtract the expectation value.

Other functions with the same call structure can be used in the detection of the TSS by passing it as fun argument in the identifyStartSites method.

See Also

Classes: TssData, TssNorm, TssResult

Methods: segmentizeCounts, normalizeCounts, identifyStartSites, get-methods, plot-methods, asRangedData-methods

Functions: subtract-functions

Data set: physcoCounts

Package: TSSi-package

Examples

args(subtractExpectation)

TSSi documentation built on May 6, 2019, 2:40 a.m.