PositionFrequencyMatrix: Accessor method for the 'PFM' slot in a 'genomicProfiles'...
In patrickCNMartin/ChIPanalyserDev: ChIPanalyser: Predicting Transcription Factor Binding Sites
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Accessor method for the PFM slot in a
genomicProfiles object
Usage
1
PositionFrequencyMatrix(object)
Arguments
object
object is a genomicProfiles object
Details
After creating a genomicProfiles object,
it is possible to access the Position Frequency Matrix slot.
However this slot will be empty if the genomicProfiles
object was built using directly a Position Weight Matrix.
See genomicProfiles
Value
Returns the Position Frequency Matrix (PFM slot) used to compute the
PositionWeightMatrix in a
genomicProfiles 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
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#Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building genomicProfiles object
GPP<-genomicProfiles(PFM=PFM,PFMFormat="raw")
# Accessing Slot
PositionFrequencyMatrix(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 the PFM slot in a
genomicProfiles object
Usage
1 | PositionFrequencyMatrix(object)
|
Arguments
object |
|
Details
After creating a genomicProfiles object,
it is possible to access the Position Frequency Matrix slot.
However this slot will be empty if the genomicProfiles
object was built using directly a Position Weight Matrix.
See genomicProfiles
Value
Returns the Position Frequency Matrix (PFM slot) used to compute the
PositionWeightMatrix in a
genomicProfiles 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 8 | #Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building genomicProfiles object
GPP<-genomicProfiles(PFM=PFM,PFMFormat="raw")
# Accessing Slot
PositionFrequencyMatrix(GPP)
|
R Package Documentation
Browse R Packages
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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