TSSi (version 1.18.0)

subtract-functions: Subtract functions

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)