A Minimal Book Example
1
Foreward
2
Introduction
2.1
Data Extraction and Setup
2.2
HDF5 and Loom input
2.3
Tapestri Package
2.4
Post processing
2.5
Assessing clonal abundance
3
Manuscript analysis
3.1
Figure 1: Cohort characterization
3.1.1
Cohort characteristics (EF1A-D)
3.1.2
Mutation Co-occurence
3.1.3
Oncoprint: Figure 1A
3.1.4
Sample clonality: Figure 1C,E Figure 2A,B
3.1.5
Clonograph: Figure 1D
3.2
Figure 2: Clonality
3.2.1
Clonality in disease states
3.2.2
Clonality in co-mutational groups
3.2.3
Clonality assocation with VAF
3.2.4
Co-mutation and clonality
4
Figure 3: Genetic Trajectory analysis
4.1
Introductory text and philisophy of approach:
4.2
Functions for reward matrix and querying initating mutations
4.3
Executing the Analysis
4.4
Plotting the data
5
Final Words
6
Appendix
6.1
Import from Tapestri Insights
6.2
Functions
References
Published with bookdown
Single cell mutational profiling delineates clonal trajectories in myeloid malignancies
Chapter 4
Figure 3: Genetic Trajectory analysis