CNV Detection Power Calculator

Enter experimental parameters to calculate power
Select parameter to vary to generate a power curve
Advanced setings for power curve

              

              
                
                Download Raw Data
              
              
                
                Download Graph
              
            

Overview

This tool allows users to estimate the power of their sequencing experiments for CNV detection.
The formulae used for power calculations are described in: “SS”
If you find this tool useful, please consider cite our paper.

Parameters specified by user

F: the portion of the sample that contains the CNA or CNV
alpha: the significance level
L: the length of the CNA or CNV
N: the ploidy of the CNA or CNV (normal diploid regions have N=2)
W: the size of the window
l: average sequencing read length
D: haploid sequencing depth (for a diploid dataset of 30X total coverage, the haploid coverage is 15)
theta: the variance inflation factor, equal to phi*N*D*W/l
phi: the variance inflation factor

Contact

This website is maintained by Jun Li's Lab.
Please contact hanyou@umich.edu and sramdas@umich.edu for questions.

Source code

GitHub: https://github.com/shwetaramdas/cnvpoweranalysis
Shiny: https://shiny.med.umich.edu/apps/hanyou/CNV_Detection_Power_Calculator/

2019-09-16

- With the calculator now capable of generating up to 9 lines, 8 presets are adjusted to refect 6 figures in the paper

2019-08-24

- Windows size is now moved to the advanced tab and defaulted to 1, the will eliminate the jump in the power curve due to the change in the of freedom
- Theta is added as a potential variable for power curve, this allows the web calculator to generate most of the figures in the paper
- Add support for Interactive hover over to report coordinate

2019-08-20

- Add a option to add a third parameter to vary (line type)
- Adjust defualt numbers
- New option to show x=0 in the graph

2019-08-19

- Clean the old lengthy if statements in the plot function to prepare for the more complex structure.
- Add the Advanced tab
- Add new option to fix the y-axis range

2018-09-07

- Fix a bug; now the distribution method will update correctly as the user click the preset
- A new layer of checkpoints is added for the sampling process
- The UA_CPA and UA_CPAP functions are further standardized to pave the road for the possible future change
- The UA_CPA function can now communicate with the entire input dataset directly
- A new option to use phi as inflation parameter is added
- All other related settings are adjusted for the new inflation parameter phi

2018-07-20

- Improve the log scale
- 2 new presets are added
- The default values for several presets are slightly modified.
- Fix a bug in the preset selection
- All presets are reviewed, and a major revision is applied to add description and increase readability

2018-07-19

- 5 Presets are added

2018-07-18

- Update the contact information
- Update the name from “CNV Power Calculator” to “CNV Detection Power Calculator”
- Move all the inputs to the side panel on the left
- Combine all the outputs into one summary tab in the main panel
- Update various default values
- Add an option to use log scale for x-axis
- Add a button to download the graph