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

Description Usage Arguments Details Value Author(s) References Examples

Accessor Method for the drop slot in a genomicProfiles object.

1	drop(object)

object

object is a genomicProfiles object.

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).

Returns a character string with loci containing no accesible DNA.

Patrick C.N. Martin <p.martin@essex.ac.uk>

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84<e2><80><93>94.

# Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BCDSlx.pfm")
#Building data objects
GPP <- genomicProfiles(PFM=PFM,PFMFormat="raw")

# 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)