chooseNearCisFragments {Basic4Cseq} | R Documentation |
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.
chooseNearCisFragments(expData, regionCoordinates, deleteViewpoint = TRUE)
expData |
Experiment data of class |
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)