Functions subtracting the expectation value used in the identification of TSS.
1  subtractExpectation(fg, bg, indTss, pos, basal, tau, extend=FALSE)

fg 
Numeric vector with foreground. 
bg 
Numeric vector with background of the same length as

indTss 
Index vector indicating the expected TSS sites in

pos 
Positions of the reads in the segment, as given in the

basal 
See the 
tau 
See the 
extend 
Logical indicating whether the background estimates should be computed for all positions, rather than only for those with reads. 
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.
Classes:
TssData
, TssNorm
,
TssResult
Methods:
segmentizeCounts
, normalizeCounts
,
identifyStartSites
, getmethods
,
plotmethods
, asRangedDatamethods
Functions:
subtractfunctions
Data set:
physcoCounts
Package:
TSSipackage
1 
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
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