Scale4C {Scale4C} | R Documentation |
This function creates a Scale4C object. Data on the 4C-seq experiment, i.e. read counts per fragment and viewpoint coordinates, are stored and checked for plausibility.
Scale4C(viewpoint, viewpointChromosome, rawData)
viewpoint |
The experiment's viewpoint (start, single coordinate) |
viewpointChromosome |
The experiment's viewpoint Chromosome |
rawData |
Reads of the 4C-seq experiment per fragment on an interval of interest (GRanges object with position and read data) |
A Scale4C
object contains the basic information on a 4C-seq experiment
for a certain interval of interest, i.e. read counts at given positions.
See Scale4C-class
for details. Scale-space features such as
fingerprint maps or tesselation are calculated during further steps of the
analysis by the appropriate functions.
Scale4C expects the raw data to be in a simple data frame consisting of
'position' and 'reads'. importBasic4CseqData
allows to import fragment
data from Basic4Cseq for convenience, however, preparing and importing a
simple table with two columns into R is sufficient.
An instance of the Scale4C class.
Carolin Walter
# create a Scale4C object from a Basic4Cseq export table with added # viewpoint data csvFile <- system.file("extdata", "liverData.csv", package="Scale4C") liverReads <- importBasic4CseqData(csvFile, viewpoint = 21160072, viewpointChromosome = "chr10", distance = 1000000) liverData = Scale4C(rawData = liverReads, viewpoint = 21160072, viewpointChromosome = "chr10") liverData