chipSd_-: Setter methods for 'chipSd' slot in a 'parameterOptions'...

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

Setter methods for chipSd slot in a parameterOptions object.

Description

Setter methods for chipSd slot in a parameterOptions object.

Usage

chipSd(object)<-value

Arguments

object	object is parameterOptions object.
value	value is a positive nurmeric value that will be assigned to chipSd slot. Default value is 150.

Details

When computing ChIP-seq like profiles (computeChIPProfile, the occupancy values given by computeOccupancy are transformed into ChIP-seq like profiles. The average size of a ChIP-seq peak was described by Kaplan (Kaplan et al. , 2011). The average peak size is subject to variation. This variation is accounted for with chipSd. It is advised to use the standard deviation of ChIP peak width from actual ChIP-seq data. We strongly encourage to set values when building a parameterOptions object.

Value

Returns a parameterOptions object with an updated value for chipSd.

Author(s)

Patrick C.N. Martin <[e-mail]>

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

Kaplan T.,Li X.-Y.,Sabo P.J.,Thomas S.,Stamatoyannopoulos J.A., Biggin M.D., Eisen M.B. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development, PLoS Genet.,2011, vol. 7 pg. e1001290

Examples

# Building parameterOptions object
OPP <- parameterOptions()
# Setting new value for chipSd slot
chipSd(OPP) <-  250

patrickCNMartin/ChIPanalyser documentation built on Dec. 5, 2024, 9:32 a.m.