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View Code? Open in Web Editor NEWTake command of your set enrichment analyses.
Home Page: https://lianos.github.io/sparrow/
License: MIT License
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gladkiasparrow's Issues
Assertion on contrast failed
Dear maintainer, thank you for making this delightful package. I am trying to use it to perform an enrichment analysis using fits derived from a pseudobulk analysis, and am catching an error:
sparrow::seas(gsd = gsdb, x = metadata(fits.risk[[x]])$v,
design = metadata(fits.risk[[x]])$fit$design, contrast = metadata(fits.risk[[x]])$fit$contrasts[,"Risk_genotypeTRUE"],
methods = c('camera', 'fgsea'), feature.max.padj = 0.001)
Warning in .local(x, ...) :
Deactivating 140 gene sets because conformation of GeneSetDb to the target creates gene sets smaller than 2 or greater than Inf
Error in calculateIndividualLogFC(x, design, contrast, treat.lfc = treat.lfc, :
Assertion on 'contrast' failed: Must have length <= 4, but has length 5.
>
> x <- 'ATL'
> metadata(fits.risk[[x]])$fit$design
(Intercept) CohortMCD SexMale eGFR_Bx Risk_genotypeTRUE
1 1 0 1 101.727 1
2 1 1 1 23.285 1
3 1 0 0 107.653 0
4 1 1 0 78.557 0
5 1 0 1 68.520 1
6 1 0 0 64.046 0
7 1 0 1 84.839 0
8 1 1 1 61.602 0
9 1 0 1 33.666 0
10 1 0 1 19.367 1
11 1 0 1 21.972 1
12 1 1 0 80.348 0
13 1 0 1 112.467 0
14 1 0 1 57.139 1
15 1 1 1 149.864 0
16 1 0 1 114.610 1
17 1 1 0 90.385 0
18 1 0 1 79.794 1
19 1 0 1 96.773 0
attr(,"assign")
[1] 0 1 2 3 4
attr(,"contrasts")
attr(,"contrasts")$Cohort
[1] "contr.treatment"
attr(,"contrasts")$Sex
[1] "contr.treatment"
attr(,"contrasts")$Risk_genotype
[1] "contr.treatment"
> metadata(fits.risk[[x]])$fit$contrasts[,"Risk_genotypeTRUE"]
Intercept CohortMCD SexMale eGFR_Bx Risk_genotypeTRUE
0 0 0 0 1
Can you please help me understand this error message? Kindest Regards.
make `sparrow::corplot` returning `E` instead of `invisible(NULL)`
Hi Steve,
Many thanks for creating such a great package :)!
Would it be possible to make sparrow::corplot returning data (i.e. E) instead of invisible(NULL). I found the need for it while using the sparrow::corplot with cluster = TRUE and not being able to get the order of the genes.
Best,
Arek
Ensure support for new mouse MSigDB collections
As of Sept 2022, MSigDB is officially providing mouse geneset collections (MH, M1, M2, M3, M5, M8).
Let's ensure this plays nicely with the getMSigGeneSetDb and getMSigCollection functions.
Reorder parameters in seas() to put `x` first.
This function is really polymorphic over x, so this should come first.
The current function signature is:
seas <- function(gdb, x, design, contrast, ...)but should really by
seas <- function(x, gdb, design = NULL, contrast = NULL, ...)Let's bite this bullet before we release this into the wild.
Add t and z stats to edgeR/qlf results from calculateIndividualLogFC
t.stat <- sign(qlf$table$logFC) * sqrt(qlf$table$F)
z <- zscoreT(t.stat, df=qlf$df.total)Assertion on 'contrast' failed
Dear maintainer, thank you for making this delightful package. I am trying to use it to perform an enrichment analysis using fits derived from a pseudobulk analysis, and am catching an error:
sparrow::seas(gsd = gsdb, x = metadata(fits.risk[[x]])$v$E,
design = metadata(fits.risk[[x]])$fit$design, contrast = metadata(fits.risk[[x]])$fit$contrasts[,"Risk_genotypeTRUE"],
methods = c('camera', 'fgsea'), feature.max.padj = 0.001)
Warning in .local(x, ...) :
Deactivating 140 gene sets because conformation of GeneSetDb to the target creates gene sets smaller than 2 or greater than Inf
Error in calculateIndividualLogFC(x, design, contrast, treat.lfc = treat.lfc, :
Assertion on 'contrast' failed: Must have length <= 4, but has length 5.
>
> x <- 'ATL'
> metadata(fits.risk[[x]])$fit$design
(Intercept) CohortMCD SexMale eGFR_Bx Risk_genotypeTRUE
1 1 0 1 101.727 1
2 1 1 1 23.285 1
3 1 0 0 107.653 0
4 1 1 0 78.557 0
5 1 0 1 68.520 1
6 1 0 0 64.046 0
7 1 0 1 84.839 0
8 1 1 1 61.602 0
9 1 0 1 33.666 0
10 1 0 1 19.367 1
11 1 0 1 21.972 1
12 1 1 0 80.348 0
13 1 0 1 112.467 0
14 1 0 1 57.139 1
15 1 1 1 149.864 0
16 1 0 1 114.610 1
17 1 1 0 90.385 0
18 1 0 1 79.794 1
19 1 0 1 96.773 0
attr(,"assign")
[1] 0 1 2 3 4
attr(,"contrasts")
attr(,"contrasts")$Cohort
[1] "contr.treatment"
attr(,"contrasts")$Sex
[1] "contr.treatment"
attr(,"contrasts")$Risk_genotype
[1] "contr.treatment"
> metadata(fits.risk[[x]])$fit$contrasts[,"Risk_genotypeTRUE"]
Intercept CohortMCD SexMale eGFR_Bx Risk_genotypeTRUE
0 0 0 0 1
Can you please help me understand this error message? Kindest Regards.
Use babelgene package to re-implement convertIdentifiers()
We previously included species and identifier maps in this package for this function to work, but since {babelgene} (which powers {msigdbr}) is now a dependency, let's use that.
Note the original function was called remap_identifiers, but since we're using camel case here, we're going with convertIdentifiers (and "converting" is more what we are doing, not remaping (I guess? ... who knows ...))
Reorder paramters in scoreSingleSamples to put `x` first
Just like issue #5, this function is really polymorphic over x and not the GeneSetDb, so x should come first.
Wire up the seas select_by, group_by, biased_by parameters to correct downstream mojo
The select_by, group_by, and bias_by were added so we can tweak how ora was run through the seas() wrapper, but those parameters aren't used in the seas() function itself. Fix that!
seas fails when passing inputs to `ora`, & `fgsea`
A thin wrapper function implemented in gCrisprTools fails when invoking the seas command:
Create a renameCollection function
It's not too hard to rename collections by manipulating the internal data.tables, let's do that.
This code snippet renames a "C7" collection to "ImmuneSigDb" in a GeneSetDb gdb object:
gdb@db[collection == "C7", collection := "ImmuneSigDb"]
setkeyv(gdb@db, c("collection", "name", "feature_id"))
gdb@table[collection == "C7", collection := "ImmuneSigDb"]
setkeyv(gdb@table, c("collection", "name"))
gdb@collectionMetadata[collection == "C7", collection := "ImmuneSigDb"]
setkeyv(gdb@collectionMetadata, c("collection", "name"))Ideas
The function signature might look like:
renameCollection <- function(gdb, rename, ...) {
}with rename being a named character vector with names() being the current name of the collection, and its values are the new collection names you want to rename them to.
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