longitudinalData: Longitudinal validation data

In cloneRate: Estimate Growth Rates from Phylogenetic Trees

Longitudinal validation data

Description

For three individuals with clonal expansions that can be estimated using our methods, we have longitudinal data to orthogonally validate these estimates, which is included here. Additionally, for 13 clones with a driver gene matching a driver gene in the single cell data, but without a match to a specific clone, we include this longitudinal data as well.

Usage

longitudinalData

Format

A data.frame containing all the information needed

Sample.ID

The individual's ID

Age

Individual's age at the various sampling times

VAF

The variant allele frequency at the various sampling times for the clone of interest

Gene

Gene or genes with mutation that identifies the clone

Protein

Protein affected by the mutation

cellType

The type of cells used for sequencing

cloneName

The name we use for the clone to match to single cell data, if applicable.

References

These datasets were generated and annotated in: Williams et al. 2022 Fabre et al. 2022

Examples

# Plot longitudinal data from PD9478
library(ggplot2)
ggplot(longitudinalData[longitudinalData$Sample.ID == "PD9478", ]) +
  geom_point(aes(x = Age, y = VAF))

cloneRate documentation built on Sept. 22, 2023, 5:09 p.m.