BPFrequency_-: Setter method for 'BPFrequency' slot in a 'genomicProfiles'...
In ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Setter method for BPFrequency slot in a
genomicProfiles object.
If base pair frequency is unknown, BPFrequency will compute base pair
frequency from a DNA sequence.
Usage
1
BPFrequency(object)<-value
Arguments
object
object is a genomicProfiles object.
value
value can three different objects:
A vector of length 4 containing the probability of occurrence of each base
pair (A,C,G,T) in order.
Default value is c(0.25,0.25,0.25,0.25).
A BSgenome of the organism of interest. The base pair frequency will
automatically be computed and updated in
genomicProfiles.
A DNAStringSet of the organisme of interest.
The base pair frequency will automatically be computed and updated
in genomicProfiles (Prefered method).
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 when building a
genomicProfiles object.
The nature of this sequence can be aBSgenome object or a
DNAStringSet. In order to decrease run time,
it is advised to use DNAStringSet.
Value
Returns a genomicProfiles object with an updated
value for BPFrequency.
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<e2><80><93>94.
Examples
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data(ChIPanalyserData)
# path to Position Frequency Matrix
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#As an example of genome, this example will run on the Drosophila genome
if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
}
library(BSgenome.Dmelanogaster.UCSC.dm3)
DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)
# Building genomicProfiles object
GPP <- genomicProfiles(PFM=PFM, BPFrequency=DNASequenceSet)
# Updating BPFrequency
## !! Note!! BPFrequency is used to compute PWM from PFM
## IF updated after building GPP, then it will not influence PWM
## Advised to build with BPFrequency directly
BPFrequency(GPP) <- DNASequenceSet
BPFrequency(GPP) <- c(0.25,0.25,0.25,0.25)
ChIPanalyser documentation built on Nov. 8, 2020, 8:23 p.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
Setter method for BPFrequency slot in a
genomicProfiles object.
If base pair frequency is unknown, BPFrequency will compute base pair
frequency from a DNA sequence.
Usage
1 | BPFrequency(object)<-value
|
Arguments
object |
|
value |
A vector of length 4 containing the probability of occurrence of each base pair (A,C,G,T) in order. Default value is c(0.25,0.25,0.25,0.25). A A |
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 when building a
genomicProfiles object.
The nature of this sequence can be aBSgenome object or a
DNAStringSet. In order to decrease run time,
it is advised to use DNAStringSet.
Value
Returns a genomicProfiles object with an updated
value for BPFrequency.
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<e2><80><93>94.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | data(ChIPanalyserData)
# path to Position Frequency Matrix
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#As an example of genome, this example will run on the Drosophila genome
if(!require("BSgenome.Dmelanogaster.UCSC.dm3", character.only = TRUE)){
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("BSgenome.Dmelanogaster.UCSC.dm3")
}
library(BSgenome.Dmelanogaster.UCSC.dm3)
DNASequenceSet <- getSeq(BSgenome.Dmelanogaster.UCSC.dm3)
# Building genomicProfiles object
GPP <- genomicProfiles(PFM=PFM, BPFrequency=DNASequenceSet)
# Updating BPFrequency
## !! Note!! BPFrequency is used to compute PWM from PFM
## IF updated after building GPP, then it will not influence PWM
## Advised to build with BPFrequency directly
BPFrequency(GPP) <- DNASequenceSet
BPFrequency(GPP) <- c(0.25,0.25,0.25,0.25)
|
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