PFMFormat {ChIPanalyser} | R Documentation |
PFMFormat
slot in a
genomicProfileParameters
object
Accesor method for the PFMFormat
slot in a
genomicProfileParameters
object
PFMFormat(object)
object |
|
If loading a
PositionFrequencyMatrix
from a file, the format
of the file should be specified. Default is raw. Please keep in mind that
this argument is used when parsing the
PositionFrequencyMatrix
file. IF this argument is changed
after building the genomicProfileParameters
with
a PositionFrequencyMatrix file, this
will not influence the parsing of the file.
PFMFormat
can be one of the following:
"raw","transfac","JASPAR" or "sequences"
Returns the value assigned to the PFMFormat
slot a
genomicProfileParameters
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 #### THIS IS THE PREFFERED METHOD FOR SETTING PFMFormat GPP <- genomicProfileParameters(PFM=PFM,PFMFormat="raw") #Setting New value for PFMFormat PFMFormat(GPP)