processingChIPseq {ChIPanalyser} | R Documentation |
processingChIPseq
will process and extract ChIP scores at a set of loci of interest.
processingChIPseq(profile,loci=NULL,reduce=NULL, occupancyProfileParameters=NULL, peaks=NULL,Access=NULL,noiseFilter=c("zero","mean","median","sigmoid"),cores=1)
profile |
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loci |
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reduce |
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occupancyProfileParameters |
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peaks |
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Access |
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noiseFilter |
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cores |
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When using computeOptimal
, it is required to supply real ChIP
data in order to have a point of comparison. The corralation and MSE Scores are
computed based of how well the model fits biological data.
processingChIPseq
will extract this data from ChIP data at loci
of interest. When using the reduce
option, this function will only
select the top regions based on peak height or mean ChIP score.
processingChIPseq
will also extract maxSignal and backgroundSignal from
ChIP data and parse it to an occupancyProfileParameters
object.
If using reduce, will return a list of two elements.
The first element will contain a list with extracted ChIP data and a new set
of top scoring loci loci. The second element will contain a
occupancyProfileParameters
object with maxSignal
and backgroundSignal slot updated.
If NOT using reduce, the first element will only contain
ChIP score at loci of interest the second will still contain a
occupancyProfileParameters
object with maxSignal
and backgroundSignal slot updated.
Patrick C.N. Martin <pm16057@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.
#Data extraction data(ChIPanalyserData) ## Extracting ChIP scores at loci of interest ChIP<-processingChIPseq(profile=eveLocusChip, loci=eveLocus)