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.

Sign up for GitHub

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

Jump to bottom

import-rna: support -n/--normal option #362

Closed
etal opened this issue Jun 6, 2018 · 1 comment
Closed

import-rna: support -n/--normal option #362

etal opened this issue Jun 6, 2018 · 1 comment
Labels
enhancement rna

Comments

@etal
Copy link
Owner

etal commented Jun 6, 2018 •
edited
Loading

The import-rna --normal option is parsed on the CLI and values are passed around, but ultimately cnvlib.rna.normalize_read_depths doesn't do anything with it yet.

Use the specified "normal" samples' log2 values as a control.

Following the Tirosh paper, after iteratively centering by gene and by sample, subtract the normal samples' IQR with log2=0 as a floor:

  • Calculate 75%ile and 25%ile of normal samples' log2 values

  • For the non-normal (test/tumor) samples:

      T > n75          -->  T - n75
  n75 >= T >= n25  -->  0
  n25 > T          -->  T - n25

Alternatively, just subtract the rolling mean/median/biweight location of normals from the test samples.
etal added a commit that referenced this issue Jun 7, 2018
@etal
import-rna: implement -n/--normal option (#362)
a20ed89 
The option was already there, this just makes use of the given normals
-- in two ways:

1. Divide the normalized sample depths by the median of normals' depth
at each gene. (default)
2. Divide the normalized sample depths by the upper or lower quartiles
of normals' depth at each gene when sample depth is outside the normal
IQR, otherwise reset to the neutral value 1. (coded but disabled)
@etal
Copy link
Owner Author

etal commented Jun 7, 2018

Some benchmarking needs to be done to decide which of the two normalization approaches should be used. Otherwise, this is in place now.

@etal etal mentioned this issue Jun 7, 2018
Open
@etal etal closed this as completed Jun 12, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement rna
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@etal