89 gsora and gsea. #92
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jmitchell81
commented
Apr 6, 2024
jmitchell81
commented
- getPatternHallmarks changed to getPatternGeneSets
- getPatternGeneSets can conduct gene set enrichment analysis, ranking features by pattern amplitude, or gene set overrepresentation analysis, for occurrence of gene sets within pattern marker lists.
- removes usage of msigdbr to query the hallmark gene sets. Gene set inputs are now provided as lists.
- function to plot the gene set test result updated to plot either enrichment or overrepresentation under the same framework, change the title to reflect which test was used, and change the p-value threshold used to decide which gene sets are rendered on the plot.
- implements unit tests for the capability to generate gene set test results for enrichment and overrepresentation tests on the GIST data and tests the capability to generate a ggplot object from the plotting function for both test types.
Carries over overrepresentation test from getPatternHallmark
tests enrichment of gene set when ordering genes by pattern amplitude.
Tested gene sets were chosen arbitrarily as the features with the 5 lowest and highest numbers in their names. Prior tests use expect_no_error, which is not a function in my currently installed version of testhat. I will check for updates when I have internet again.
There was a fair amount of overzealous commenting from when I was first learning how to make ggplots.
Saves time and computing by not needing to rerun CoGAPS
I found that the base expect_error function can be used to test for no errors if the expected output is NA in the case there is no error.
with update of testthat to v3.2.1, I am able to use the expect_no_error function
A line will be drawn corresponding to the point on the x-axis that corresponds to an adjusted p-value of 0.05. Also accounts for pulling the data.frame used to plot the waterfall plot if a list containing one enrichment data frame is provided.
Tests that a ggplot is rendered and that the title of the plot reflects if method "overrepresentation" or "enrichment" was used.
Only the data frames inside the patterngeneset list are necessary to generate the waterfall plots. Therefore, the object arguments have been removed.
dimalvovs
requested changes
Apr 8, 2024
| @@ -20,15 +20,15 @@ export(getFeatureLoadings) | |||
| export(getMeanChiSq) | |||
| export(getOriginalParameters) | |||
| export(getParam) | |||
| export(getPatternHallmarks) | |||
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renaming needs to be done in also in /vignettes/CoGAPs.rmd to allow the package to build.
stopping review here as the R CMD build . fails
Replacement of getPatternHallmarks in vignettes now that the function had changed names. Currently uses a placeholder example of testing two hallmark gene sets known to be enriched in pattern 7. The full gene sets are written in the code executed and should be replaced with a direct query of the gene sets from online or a hosted gene set in the package. I would avoid reuse of msigdbr because dependancy on this unstable package was the impetus for these changes in the first place.
Uses the same parameters for patternMarkers as was used in the CoGAPS analysis of the PDAC atlas.
dimalvovs
approved these changes
Apr 9, 2024
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Thank you @jmitchell81 for adding tests as well as examples to the vignette. LGTM.
This was referenced Apr 9, 2024
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