Fix dsfdr and load repseqs from qiime2 #168
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Collaborator
amnona
commented
Nov 27, 2019
amnona
commented
- Load repseqs file from qiime2 qza if supplied
- fix a bug in dsfdr when using a user supplied statist for dsfdr - we didn't take the abs() of the effect size so would only look for positive extreme effect size
RNAer
reviewed
Dec 18, 2019
calour/io.py
Outdated
| logger.info('Rep seqs hashes and table hashes are not equal. Using table hashes.') | ||
| newexp.feature_metadata.rename(columns={'_feature_id': '_hash'}, inplace=True) | ||
| newexp.feature_metadata = newexp.feature_metadata.join(other=rep_seqs, on='_hash', how='left') | ||
| newexp.feature_metadata.set_index('_feature_id', inplace=True, drop=False) | ||
|
|
There was a problem hiding this comment.
what does this change diff?
There was a problem hiding this comment.
This was added so the sequences (and not the hashes) are the _feature_id and index
(added comment in file)
| @@ -292,11 +291,13 @@ def dsfdr(data, labels, transform_type='rankdata', method='meandiff', | |||
| # call the user-defined function of statistical test | |||
| t = method(data, labels) | |||
| tstat = t.copy() | |||
| t = np.abs(tstat) | |||
There was a problem hiding this comment.
why need to be absolute value? could you add comment to explain?
There was a problem hiding this comment.
We need abs() since dsFDR performs a two-sided test. added comment in file.
|
comments addressed. @RNAer - ready for merge? |
|
there are conflicts |
|
fixed the conflict (don't know why it created the conflict - same line in both versions....) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.