genomicProfileParameters {ChIPanalyser} | R Documentation |
genomicProfileParameter
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
.
genomicProfileParameters(PWM = NULL, PFM = NULL,PFMFormat="raw", ScalingFactorPWM = 1, PWMpseudocount = 1, noOfSites = 0, BPFrequency = rep(0.25, 4), naturalLog = FALSE, PWMThreshold = 0.7, strandRule = "max", whichstrand = "+-")
PFM |
|
PWM |
|
PFMFormat |
|
ScalingFactorPWM |
|
PWMpseudocount |
|
BPFrequency |
|
naturalLog |
|
noOfSites |
|
PWMThreshold |
|
strandRule |
|
whichstrand |
|
Most functions in ChIPanalyser
require some form of a
genomicProfileParameters
object. It is required to build a
genomicProfileParameters object before starting any computation.
Most functions will return a genomicProfileParameters and thus this
object should be parsed to the next function and so on. Most parameters
are customisable and we strongly advise to do so. This can either be
done directly (advised method) when building the
genomicProfileParameters
or by using setter methods.
The former is advised as certain value are computed internally and
require that parameters are set before hand ( e.g BPFrequency
).
It is important to note that not all slots/parameters can be set by user.
The value assinged to these slots are computed internally.
For more information on this slots, see
genomicProfileParameters-class
.
The following describes the default values and which slot are
computed internally:
PWM = To be supplied by user
PFM = To be supplied by user
PFMFormat ="raw"
ScalingFactorPWM = 1
PWMpseudocount = 1
BPFrequency = c(0.25,0.25,0.25,0.25)
naturalLog = TRUE
noOfSites = 0
minPWMScore = Internally Computed
maxPWMScore = Internally Computed
PWMThreshold = 0.7
AllSitesAboveThreshold = Internally Computed
DNASequenceLength = Internally Computed (may still be provided by user see
DNASequenceLength<-
)
averageExpPWMScore = Internally Computed
strandRule = ‘max’
whichstrand = ‘+-’
NoAccess = Internally Computed
ZeroBackground = Internally Computed
Returns a genomicProfileParameters
object
Patrick 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-class
occupancyProfileParameters
occupancyProfileParameters-class
#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)){ source("https://bioconductor.org/biocLite.R") biocLite("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)