PositionWeightMatrix: Accessor Method for the 'PWM' 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 PWM slot in a
genomicProfiles object
Usage
1
PositionWeightMatrix(object)
Arguments
object
object is a genomicProfiles
Details
After creating a genomicProfiles object,
it is possible to access the Position Weight Matrix stored in this slot.
This slot should always contain something. This slot is either supplied by
user or directly computed from a Position Frequency Matrix when supplied.
Value
Returns a matrix in the form of a Position Weight Matrix
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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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
PositionWeightMatrix(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 PWM slot in a
genomicProfiles object
Usage
1 | PositionWeightMatrix(object)
|
Arguments
object |
|
Details
After creating a genomicProfiles object,
it is possible to access the Position Weight Matrix stored in this slot.
This slot should always contain something. This slot is either supplied by
user or directly computed from a Position Frequency Matrix when supplied.
Value
Returns a matrix in the form of a Position Weight Matrix
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
PositionWeightMatrix(GPP)
|
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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