Diann update #182
Merged
Diann update #182
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
refactor DIA-NN step 1
restruct DIA-NN step2
Co-authored-by: Julianus Pfeuffer <[email protected]>
Co-authored-by: Julianus Pfeuffer <[email protected]>
Restruct DIA-NN step 3,4,5
� Conflicts: � bin/msstats_tmt.R � modules/local/silicolibrarygeneration/main.nf
|
jpfeuffer
requested changes
May 17, 2022
Comment on lines
+251
to
+255
| require(MSstats) | ||
| # BUG groupComparisonPlots function: re-run OpenMStoMSstatsTMTFormat | ||
| quant <- OpenMStoMSstatsTMTFormat(data, useUniquePeptide=useUniquePeptide, rmPSM_withfewMea_withinRun=rmPSM_withfewMea_withinRun, | ||
| rmProtein_with1Feature=rmProtein_with1Feature | ||
| ) |
There was a problem hiding this comment.
What is this? quant is never used after that. And why is MSstats loaded?
There was a problem hiding this comment.
If MSstats is needed for those plots, it needs to go into the dependencies!
There was a problem hiding this comment.
@daichengxin can you take care of this comment. Please do your changes in the diann branch.
| @@ -246,5 +241,28 @@ if (l == 1) { | |||
| test.MSstatsTMT <- groupComparisonTMT(contrast.matrix=contrast_mat, data=processed.quant) | |||
There was a problem hiding this comment.
If you do parse_contrasts, the TODO can go
There was a problem hiding this comment.
@daichengxin can you take care of this comment. Please do your changes in the diann branch.
| description: FASTA sequence databases | ||
| pattern: "*.{fasta,fa}" | ||
| - cfg: | ||
| description: Silico-predicted spectral library by deep leaning predictor in DIA-NN |
There was a problem hiding this comment.
Isn't this using the empirical library?? Not the initially predicted one
Co-authored-by: Julianus Pfeuffer <[email protected]>
Co-authored-by: Julianus Pfeuffer <[email protected]>
Co-authored-by: Julianus Pfeuffer <[email protected]>
Co-authored-by: Julianus Pfeuffer <[email protected]>
Co-authored-by: Julianus Pfeuffer <[email protected]>
|
LFQ is failing @daichengxin |
|
Weird, seems to work now. Conda hiccups are normal though. |
|
@jpfeuffer Can I merge now and convert your comments into issue ;) |
|
Yes:
|
|
#183 issue created by @jpfeuffer |
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.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).