PWMpseudocount: Accessor Method for a 'PWMpseudocount' slot in a...
In patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Accessor Method for a PWMpseudocount slot in a
parameterOptions
Usage
1
PWMpseudocount(object)
Arguments
object
object is a parameterOptions object.
Details
In the context of Position Weight Matricies, the pseudocount is used
to avoid 0 probabilities during the transformation of
Position Frequency Matrix to a Position Probability Matrix and finally to a
Postion Weight Matrix. It is essentially a sample correction that is added
in the case of small sample size. The effect of the base pair to which a
pseudocount was assigned will not influence the model nor will create
mathematical issues such as infinities or zero division. Default is set at 1.
Value
Returns the value assigned to a PWMpseudocount slot in a
parameterOptions object
Author(s)
Patrick C. N. Martin <pm16057@essex.ac.uk>
References
Zabet NR, Adryan B (2015) Estimating binding properties of transcription
factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
Examples
1
2
3
4
5
6
7
# Loading data
data(ChIPanalyserData)
#Building data objects
GPP <- parameterOptions(PWMpseudocount=0)
#Accessing slot value
PWMpseudocount(GPP)
patrickCNMartin/ChIPanalyserDev documentation built on Nov. 14, 2019, 4:39 p.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
Accessor Method for a PWMpseudocount slot in a
parameterOptions
Usage
1 | PWMpseudocount(object)
|
Arguments
object |
|
Details
In the context of Position Weight Matricies, the pseudocount is used to avoid 0 probabilities during the transformation of Position Frequency Matrix to a Position Probability Matrix and finally to a Postion Weight Matrix. It is essentially a sample correction that is added in the case of small sample size. The effect of the base pair to which a pseudocount was assigned will not influence the model nor will create mathematical issues such as infinities or zero division. Default is set at 1.
Value
Returns the value assigned to a PWMpseudocount slot in a
parameterOptions object
Author(s)
Patrick C. N. Martin <pm16057@essex.ac.uk>
References
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
Examples
1 2 3 4 5 6 7 | # Loading data
data(ChIPanalyserData)
#Building data objects
GPP <- parameterOptions(PWMpseudocount=0)
#Accessing slot value
PWMpseudocount(GPP)
|
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