Add formula based contrasts to deseq2
#8569
Conversation
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I am not sure why only the conda test is failing even after setting seed. Any ideas how to move forward? |
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It's probably just floating point differences (IIRC there are rounding controls somewhere to help). If you can, run with Docker and conda and compare the files to be sure. |
| @@ -112,7 +125,8 @@ opt <- list( | |||
| cores = 1, | |||
| vs_blind = TRUE, | |||
| vst_nsub = 1000, | |||
| round_digits = NULL | |||
| round_digits = NULL, | |||
| seed = 1 | |||
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I remember @pinin4fjords had a strong opinion on not setting a seed unless explicitly specified.
Can this default to NULL instead, and the set.seed below is only triggered if the seed is not NULL?
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Yes, I will disagree strongly with folks who set seeds by default. The reason is that it gives unrealistic impressions of reproducibility. It's only valid in testing scenarios IMO
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Yes this had to be added for testing purposes only but I agree we can set this to NULL and then pass the arg in that test case.
| @@ -281,22 +305,30 @@ if ((is_valid_string(opt\$exclude_samples_col)) && (is_valid_string(opt\$exclude | |||
| # Now specify the model. Use cell-means style so we can be explicit with the | |||
| # contrasts | |||
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| model <- '~ 0' | |||
| if (is_valid_string(opt\$formula)) { | |||
| ) | ||
| ) | ||
| } | ||
| } else { | ||
| comp.results <- |
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pls fix indentation / consider autoformatting with air/styler
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I have the settings json file with
"[r]": {
"editor.formatOnSave": true
}
but it doesn't seem to work, neither running air format . due to Failed to parse due to syntax errors. which stems from all opt$ having the backlash opt\$
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ah, I see. That's correct, both formatters will only work on parsable syntax :/
…into formula_deseq2
nf-core/differentialabundance#459
Draft POC / work in progress
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