PFMFormat<- | R Documentation |
PFMFormat
slot in a
genomicProfiles
object
Setter method for the PFMFormat
slot in a
genomicProfiles
object
PFMFormat(object) <- value
object |
|
value |
|
If loading a
PositionFrequencyMatrix
from a file, the format
of the file should be specified. Default is JASPAR. Please keep in mind that
this argument is used when parsing the
PositionFrequencyMatrix
file. IF this argument is changed
after building the genomicProfiles
with
a PositionFrequencyMatrix file, this
will not influence the parsing of the file.
Returns a genomicProfiles
object with an updated
value for the PFMFormat
slot.
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. Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.
# Loading data
data(ChIPanalyserData)
#Loading PFM files
PFM <- file.path(system.file("extdata",package="ChIPanalyser"),"BEAF-32.pfm")
#Building data objects
#### THIS IS THE PREFFERED METHOD FOR SETTING PFMFormat
GPP <- genomicProfiles(PFM=PFM,PFMFormat="JASPAR")
#Setting New value for PFMFormat
PFMFormat(GPP) <- "JASPAR"
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.