BPFrequency: Accessor method for 'BPFrequency' slot in a 'genomicProfiles'...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites
BPFrequency R Documentation
Accessor method for BPFrequency slot in a
genomicProfiles object.
Description
Extract or Access BPFrequency slot in a
genomicProfiles object.
Usage
BPFrequency(object)
Arguments
object
object is a genomicProfiles
Details
Default value is c(0.25,0.25,0.25,0.25)
When generating a Postion Weight Matrix from a Position Frequency Matrix,
the probability
of occurrence of each base pair (Base Pair Frequency) is necessary
(as originally described by Gary Stormo). It is possible to
set custom values for BPFrequency with a vector of length 4
containing the probability of occurrence of each base pair (A,C,G,T) in order.
If Base pair frequency is unknown, BPFrequency will compute base pair
frequency from a DNA sequence. The nature of this sequence can be a
BSgenome or a DNAStringSet.
In order to decrease run time, it is advised to use
DNAStringSet
Value
Returns BPFrequency slot in
genomicProfiles object.
Author(s)
Patrick C.N. Martin <pcnmartin@gmail.com>
References
Zabet NR, Adryan B (2015) Estimating binding properties of transcription
factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
Examples
data(ChIPanalyserData)
# path to Position Frequency Matrix
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BEAF-32.pfm")
# Building genomicProfiles object
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR")
#Extracting BPFrequency slot
BPFrequency(GPP)
patrickCNMartin/ChIPanalyser documentation built on Nov. 24, 2022, 12:02 a.m.
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| BPFrequency | R Documentation |
Accessor method for BPFrequency slot in a
genomicProfiles object.
Description
Extract or Access BPFrequency slot in a
genomicProfiles object.
Usage
BPFrequency(object)
Arguments
object |
|
Details
Default value is c(0.25,0.25,0.25,0.25)
When generating a Postion Weight Matrix from a Position Frequency Matrix,
the probability
of occurrence of each base pair (Base Pair Frequency) is necessary
(as originally described by Gary Stormo). It is possible to
set custom values for BPFrequency with a vector of length 4
containing the probability of occurrence of each base pair (A,C,G,T) in order.
If Base pair frequency is unknown, BPFrequency will compute base pair
frequency from a DNA sequence. The nature of this sequence can be a
BSgenome or a DNAStringSet.
In order to decrease run time, it is advised to use
DNAStringSet
Value
Returns BPFrequency slot in
genomicProfiles object.
Author(s)
Patrick C.N. Martin <pcnmartin@gmail.com>
References
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
Examples
data(ChIPanalyserData)
# path to Position Frequency Matrix
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BEAF-32.pfm")
# Building genomicProfiles object
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR")
#Extracting BPFrequency slot
BPFrequency(GPP)
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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