Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

switch from absolute tolerance to relative? #131

Closed
golobor opened this issue Sep 6, 2018 · 3 comments
Closed

switch from absolute tolerance to relative? #131

golobor opened this issue Sep 6, 2018 · 3 comments

Comments

@golobor
Copy link
Member

golobor commented Sep 6, 2018

according to the code, currently, tolerance is specified in the units of #contacts.

An attempt to trace units:
line 135: margs are in the units of #contacts (i.e. proportional to # of reads in the library)
line 145: nzmargs are in the units of margs (#contacts)
line 156: var in the units of nzmargs (#contacts)
line 167: tol is compared to var

importantly, margs are re-computed using biases, but biases average out to 1.0, so margs first come out in the units of #contacts

Specifying tol in relative units makes more sense since it is hard for the user to know the # of reads in the library before balancing. We can still keep the option to specify an absolute tolerance, but I would argue that relative tolerance is a better default.

@golobor
Copy link
Member Author

golobor commented Jan 7, 2019

bump?

@golobor
Copy link
Member Author

golobor commented Mar 11, 2019

bump

@nvictus nvictus mentioned this issue Jun 30, 2020
5 tasks
@nvictus
Copy link
Member

nvictus commented Jun 30, 2020

See #210

@nvictus nvictus closed this as completed Jun 30, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants