strandRule<- {ChIPanalyser} | R Documentation |
strandRule
slot in a
genomicProfileParameters
object.
Setter method for the strandRule
slot in a
genomicProfileParameters
object.
strandRule(object) <- value
object |
|
value |
|
When computing the PWM Scores and if whichstrand
is set
to ‘+-’, strandRule
will determine how to handle both strands
( one of three options : ‘mean’, ‘max’, ‘sum’). If set to ‘mean’,
the average PWM Score of both strand will be computed. If set to ‘max’,
the highest PWM score between each strand will be selected and finally ‘sum’
will sum both score together.
Default set at ‘max’
Returns a genomicProfileParameters
object with an updated
value for the strandRule
slot
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.
# Loading data data(ChIPanalyserData) #Loading PFM files PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm") #Building data objects GPP <- genomicProfileParameters(PFM=PFM, strandRule="max") #Setting New Value for strandRule strandRule(GPP) <- "mean"