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.
The experiment's viewpoint (start, single coordinate)
The experiment's viewpoint Chromosome
Reads of the 4C-seq experiment per fragment on an interval of interest (GRanges object with position and read data)
Scale4C object contains the basic information on a 4C-seq experiment
for a certain interval of interest, i.e. read counts at given positions.
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.
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# 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
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