chooseNearCisFragments: Choose fragments in a provided region around the viewpoint

Description Usage Arguments Value Note Author(s) Examples

Description

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.

Usage

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chooseNearCisFragments(expData, regionCoordinates, deleteViewpoint = TRUE)

Arguments

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

Value

A data frame containing the chosen near-cis fragments

Note

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.

Author(s)

Carolin Walter

Examples

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

Basic4Cseq documentation built on Nov. 8, 2020, 6:53 p.m.