TCR dist

[grst]

In GitLab by @grst on Jan 24, 2020, 13:50

Getting the alignments was quite straightforward, thanks to parasail.
We said that we focus on CDR3, at least initially.

@szabogtamas, some points to discuss

• Distance between which chains? primary alpha/beta only?
• What if a cell does not have either alpha or beta?
• Right now, I use blosum62 to compute the alignment score. I think in the original publication they cap the max score per amino acid to 4. Does that make sense?

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Edit:
Prototype works. ToDo for now.

• Add clonotype overlap as a distance metric (simple 0-1)
• keyword argument to choose to compute on primary_only or all chains
• consider TRA and TRB separately.

[grst]

In GitLab by @szabogtamas on Jan 24, 2020, 20:23

I think we could leave the decision up to the user. One option would be to ignore secondary chains. The other option would be to have four distances between each pair of cells:

• TRA1/TRB1
• TRA2/TRB1
• TRA1/TRB2
• TRA2/TRB2
  Then we could take the minimum of that four as the distance metric (or even the maximum makes sense in some cases).
  Just like for sequence logos, I would go with an 'XXXXXXXXXXXXXX' seqeunce. This works well with the current implementation already, making the similarity score as low as possible.

The last point I don't really get. They must have a rationale behind capping the score but for me it would be more logical to use alignment scores as they are... I will try to look into the paper again.

[grst]

In GitLab by @grst on Jan 30, 2020, 11:03

changed the description

[grst]

In GitLab by @szabogtamas on Feb 12, 2020, 13:37

Add clonotype overlap as a distance metric.

[grst]

In GitLab by @szabogtamas on Feb 12, 2020, 13:47

[removed]

[grst]

In GitLab by @grst on Feb 14, 2020, 16:13

changed the description

[grst]

In GitLab by @grst on Feb 14, 2020, 16:19

mentioned in merge request !10

[grst]

In GitLab by @grst on Feb 14, 2020, 16:19

assigned to @grst

[grst]

In GitLab by @grst on Feb 28, 2020, 09:10

marked the task Add clonotype overlap as a distance metric (simple 0-1) as completed

[grst]

In GitLab by @grst on Feb 28, 2020, 12:51

closed via merge request !10

[grst]

In GitLab by @grst on Feb 28, 2020, 12:51

mentioned in commit 3c73cbb