strandRule<- {ChIPanalyser}R Documentation

Setter method for the strandRule slot in a genomicProfileParameters object.

Description

Setter method for the strandRule slot in a genomicProfileParameters object.

Usage

strandRule(object) <- value

Arguments

object

object is a genomicProfileParameters object

value

value is a character string and can be one of the following ‘mean’, ‘max’, ‘sum’. This will only apply if whichstrand is ‘+-’. Default set at ‘max’

Details

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’

Value

Returns a genomicProfileParameters object with an updated value for the strandRule slot

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, 84–94.

Examples

# 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"
[Package ChIPanalyser version 1.2.0 Index]