feat: add formula and contrasts to limma #8429
Draft
Conversation
This file contains hidden or 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
| if (!is.null(opt\$formula)) { | ||
| model <- opt\$formula | ||
| } else { | ||
|
|
| @@ -393,6 +415,9 @@ fit <- do.call(lmFit, lmfit_args) | |||
| # Contrasts bit | |||
|
|
|||
| # Create the contrast string for the specified comparison | |||
| if (!is.null(opt\$contrast_string)) { | |||
| contrast_string <- opt\$contrast_string | |||
| } else { | |||
There was a problem hiding this comment.
Again, indents for conditional
| file(params.modules_testdata_base_path + "genomics/homo_sapiens/array_expression/GSE38751.csv", checkIfExists: true) | ||
| ] | ||
| ) | ||
| input[0] = Channel.of(['id': 'diagnosis_normal_uremia', 'variable': 'diagnosis', 'reference': 'normal', 'target': 'uremia', 'formula': '~ diagnosis', 'comparison': 'diagnosis.uremia']) |
There was a problem hiding this comment.
Should this test maybe have null target etc to ensure they're not being used?
There was a problem hiding this comment.
Indeed, this is a very good observation that led me to realise a few things about the current design.
| @@ -72,6 +72,130 @@ nextflow_process { | |||
| ) | |||
| } | |||
|
|
|||
| } | |||
|
|
|||
| test("test_limma_differential - null formula and null complex contrasts") { | |||
There was a problem hiding this comment.
Needs an indent fix. Sorry if I'm not seeing it, but isn't this the same as one of the tests above?
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Outdated suggestions cannot be applied.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.
nf-core/differentialabundance#458
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda