make.clonal.data.frame: Create a data frame to hold clonal structure of a single...
In hdng/clonevol: Clonal ordering and visualization

Description Usage Arguments Details

Create a data frame ready for clonal structure enumeration. This data frame will hold VAFs of variant clusters, descending order, together with other additional columns convenient for clonal structure enumeration.

1	clones.df = make.clonal.data.frame(vafs, labels, add.normal=FALSE)

`vafs:`	VAFs of the cluster (values from 0 to 0.5)
`labels:`	labels of the cluster (ie. cluster numbers)
`add.normal:`	if TRUE, normal cell clone will be added as the superclone (ie. the founding clones will be originated from the normal clone). This is used only in polyclonal models where clones can be independently founded clones as long as their total VAFs <= 0.5. Default = FALSE
`founding.label:`	label of the founding cluster/clone

Output will be a data frame consisting of the following columns vaf: orginial VAF lab: labels of clusters occupied: how much VAF already be occupied by the child clones (all zeros) free: how much VAF is free for other clones to fill in (all equal original VAF) color: colors to plot (string) parent: label of the parent clone (all NA, will be determined in enumerate.clones)

hdng/clonevol documentation built on May 17, 2019, 3:19 p.m.