chooseNearCisFragments: Choose fragments in a provided region around the viewpoint
In Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Description Usage Arguments Value Note Author(s) Examples

This function extracts fragment data from a Data4Cseq object's rawFragments slot for visualization with the functions visualizeViewpoint and drawHeatmap . Relevant fragments are located within the chosen visualization range; the viewpoint itself can be excluded or included.

1	chooseNearCisFragments(expData, regionCoordinates, deleteViewpoint = TRUE)

`expData`	Experiment data of class `Data4Cseq` with information on the 4C-seq experiment, including fragment data for the viewpoint chromosome
`regionCoordinates`	Interval on the viewpoint chromosome for the intended visualization
`deleteViewpoint`	If TRUE, delete all fragments that intersect with the experiment's viewpoint interval

A data frame containing the chosen near-cis fragments

Viewpoint fragments are removed per default to prevent bias through overrepresented sequences caused by self-ligation. These fragments can be included, but should be interpreted with caution.

Carolin Walter

    # read example data
    data(liverData)
    fragments<-chooseNearCisFragments(liverData, regionCoordinates = c(20800000, 21000000))
    head(fragments)