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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.