drop: Accessor Method for the 'drop' slot in a 'genomicProfiles'...
In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

drop	R Documentation

Accessor Method for the `drop` slot in a `genomicProfiles` object.

Description

Accessor Method for the drop slot in a genomicProfiles object.

Usage

drop(object)

Arguments

object

object is a genomicProfiles object.

Details

During certain computations, it is possible that the Loci of interest do no show any overlap with accesible DNA. If this were to be the case, a warning message will appear in the console but these inaccessible Loci will be stored in this slot. It is also for these reasons that it is imperative for Loci of interest to be named (in this case, a named GRanges).

Value

Returns a character string with loci containing no accesible DNA.

Author(s)

Patrick C.N. Martin <p.martin@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"),"BEAF-32.pfm")
#Building data objects
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR")

# Loci with no acces - a warning message will be issued
#if loci do no contain accesible DNA
# Otherwise this slot will remain empty

drop(GPP)

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