genomicProfileParameters-class {ChIPanalyser} | R Documentation |
"genomicProfileParameters"
genomicProfileParameters
is a data/parameter storing object.
The main purpose of this object is to store parameters neccessary for
further computation but also store results. This makes parsing data and
parameters easier between the different of functions available in
ChIPanalyser
.
Objects can be created by calls of the form
genomicProfileParameters(PWM, PFM,PFMFormat,
ScalingFactorPWM, PWMpseudocount,
BPFrequency, naturalLog, noOfSites, minPWMScore,
maxPWMScore, PWMThreshold, AllSitesAboveThreshold,
DNASequenceLength , averageExpPWMScore , strandRule ,
whichstrand, NoAccess)
. PWM
and PFM
slots are the only
slots that are absolutely required (At least one of the two).
All other slots have a provided default value.
We strongly advise you to tailor these parameters to increase goodness
of fit between the predcited model and real ChIP-seq data.
PWM
:Object of class "matrix"
:
A Position Weight Matrix (either supplied or internally computed if
PFM is provided)
PFM
:Object of class "matrix"
:
A Position Frequency Matrix (may also be a path to file containing PFM)
PFMFormat
:Object of class "character"
:
A character string of one of the following: raw, transfac,JASPAR or
sequences
ScalingFactorPWM
:Object of class "vector"
:
A vector (or single value) contaning values for the ScalingFactorPWM
(Also known as lambda).Default:1
PWMpseudocount
:Object of class "numeric"
:
A numeric value describing a PWMpseudocount for PWM computation.
Default:1
BPFrequency
:Object of class "vector"
:
Base Pair Frequency in the genome (if a DNA sequence is provided
(as a DNAStringSet
or BSgenome
),
will be automatically computed internally). Default:c(0.25,0.25,0.25,0.25)
naturalLog
:Object of class "logical"
:
A logical value describing if natural Log will be used to compute
the PWM (if FALSE then log2 will be used). Default: TRUE
noOfSites
:Object of class "vector"
:
A Positive integer descibing number of sites (in base pair) should
be used from the PFM to compute PWM. Default =0 (Full width of
binding site will be used when set to 0)
minPWMScore
:Object of class "vector"
:
Lowest PWM score accros the genome (computed and updated internally)
maxPWMScore
:Object of class "vector"
:
Highest PWM score across the genome (computed and updated internally)
PWMThreshold
:Object of class "numeric"
:
Threshold at which PWM Score should be selected (only sites above
threshold will be selected - between 0 and 1)
AllSitesAboveThreshold
:Object of class "GRList"
:
Containins GRanges with sites above threshold and associated metrics
(PWMscore and Occupancy) - Computed Internally
DNASequenceLength
:Object of class "vector"
:
Length of the Genome (or accesible genome) - computed internally
averageExpPWMScore
:Object of class "vector"
:
Average exponential PWM score across the genome
(or accesible genome) - computed internally
strandRule
:Object of class "character"
:
"mean", "max" or "sum" will dertermine how strand should be handle
for computing PWM Scores. Default : "max"
whichstrand
:Object of class "character"
:
"+","-" or "+-" on which strand should PWM Score be computed.
Default: "+-"
NoAccess
:Object of class "vector"
:
Stores Loci that do contain accesible DNA if it were to be the case
(computed and updated internally)
ZeroBackground
:Object of class "vector"
:
Internal background value (computed internally)
Class occupancyProfileParameters
, directly.
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "vector")
:Slot Setter Method
signature(object =
"genomicProfileParameters", value = "DNAStringSet")
:Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "vector")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "logical")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "vector")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "matrix")
: Slot Setter Method
signature(object =
"genomicProfileParameters", value = "character")
: Slot Setter Method
signature(object =
"genomicProfileParam"
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "character")
: Slot Setter Method
signature(object =
"genomicProfileParam"
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "matrix")
:Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
:Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "numeric")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "vector")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "character")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
signature(object =
"genomicProfileParameters", value = "character")
: Slot Setter Method
signature(object =
"genomicProfileParameters")
: Slot Accessor Method
Partick C. N. Martin <p.martin@essex.ac.uk>
Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.
genomicProfileParameters
occupancyProfileParameters-class
occupancyProfileParameters
#Data extraction 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 genomicProfileParameters object GPP <- genomicProfileParameters(PFM=PFM, ScalingFactorPWM=c(1,1.5,2), BPFrequency=DNASequenceSet)