importBasic4CseqData {Scale4C} | R Documentation |
A convenience function to easily include Basic4Cseq output data into
Scale4C, importBasic4CseqData
extracts valid fragments or valid
fragment ends from a typical Basic4Cseq output table.
importBasic4CseqData(rawFile, viewpoint, viewpointChromosome, distance, useFragEnds = TRUE)
rawFile |
Name for the raw file |
viewpoint |
Viewpoint position: only fragments around a certain point of interest are imported (doesn't have to be the actual viewpoint of the experiment, though) |
viewpointChromosome |
Viewpoint chromosome of the experiment |
distance |
Distance from the viewpoint: ony fragments within a certain distance of the viewpoint are imported |
useFragEnds |
If TRUE, use full fragment end data, if FALSE, merge fragmentStart and fragmentEnd to a single item per fragment |
importBasic4CseqData
is a convenience function to import data from
Basic4Cseq. It can be ignored altogether if raw experimental data is
imported from another source or with another function into R.
A GRanges object that includes the experiment's raw data for further processing
Carolin Walter
csvFile <- system.file("extdata", "liverData.csv", package="Scale4C") liverReads <- importBasic4CseqData(csvFile, viewpoint = 21160072, viewpointChromosome = "chr10", distance = 1000000) head(liverReads)