normaliseOtherEnds {Chicago} | R Documentation |
Compute s_i
normalisation factors for other ends, and normalised counts.
normaliseOtherEnds(cd, Ncol = "NNb", normNcol = "NNboe", plot = TRUE, outfile = NULL)
cd |
A |
Ncol |
The name of an input column in |
normNcol |
The name of an output column that will contain counts normalised by other ends (in addition to any normalisation already performed on the |
plot |
If |
outfile |
|
A chicagoData
object: intData(cd)
gains new columns s_i
, and normalised output NNboe
(unless the normNcol
parameter is altered).
An object of class chicagoData
.
The object intData(cd)
is updated by reference. Thus, intData(cd)
will be altered. See vignette for further information.
Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett
##FIXME: example can be run by loading data package if it is installed, once it exists if("PCHiCdata" %in% rownames(installed.packages())) { library(PCHiCdata) data(smESC) ##modifiy smESC to use correct design directory designDir <- file.path(system.file("extdata", package="PCHiCdata"), "mm9TestDesign") smESC <- modifySettings(cd=smESC, designDir=designDir) ##normalise here... normaliseOtherEnds(smESC) } else { warning("Please install the PCHiCdata package to run this example.") }