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chuiqin / irGSEA

The integration of single cell rank-based gene set enrichment analysis
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error in irGSEA.score #12

Open zy-199326 opened 1 year ago

zy-199326 commented 1 year ago

irGSEA.score(

  • object = all_revised,
  • assay = "RNA",
  • slot = "data",
  • min.cells = 3,
  • min.feature = 0,
  • seeds = 123,
  • ncores = 10,
  • custom = F,
  • geneset = NULL,
  • msigdb = T,
  • species = "Homo sapiens",
  • category = "C5",
  • subcategory = NULL,
  • geneid = "symbol",
  • method = c("AUCell", "UCell", "singscore", "ssgsea"),
  • aucell.MaxRank = 5000,
  • ucell.MaxRank = 5000,
  • kcdf = "Gaussian"
  • )

Validating object structure Updating object slots Ensuring keys are in the proper strucutre Ensuring feature names don't have underscores or pipes Object representation is consistent with the most current Seurat version No genes remaining in following genesets: GOBP_FLAVONE_METABOLIC_PROCESS, GOBP_FLAVONOID_GLUCURONIDATION, GOBP_FORMATION_OF_QUADRUPLE_SL_U4_U5_U6_SNRNP, GOBP_NEGATIVE_REGULATION_OF_CELL_CHEMOTAXIS_TO_FIBROBLAST_GROWTH_FACTOR, GOBP_NEGATIVE_REGULATION_OF_INTERLEUKIN_21_PRODUCTION, GOBP_NEGATIVE_REGULATION_OF_MYOBLAST_PROLIFERATION, GOBP_NEGATIVE_REGULATION_OF_VASCULAR_ENDOTHELIAL_GROWTH_FACTOR_PRODUCTION, GOBP_REGULATION_OF_PRESYNAPTIC_MEMBRANE_POTENTIAL, GOBP_RETINOIC_ACID_CATABOLIC_PROCESS, GOBP_XENOBIOTIC_GLUCURONIDATION, GOMF_ESTROGEN_2_HYDROXYLASE_ACTIVITY, GOMF_GLYCINE_N_ACYLTRANSFERASE_ACTIVITY, GOMF_TRACE_AMINE_RECEPTOR_ACTIVITY, GOMF_TYPE_I_INTERFERON_RECEPTOR_BINDING, HP_HYPERCHLORIDURIA, HP_ORTHOKERATOTIC_HYPERKERATOSIS Calculate AUCell scores Error in .local(exprMat, plotStats, nCores, mctype, keepZeroesAsNA, verbose, : unused argument (splitByBlocks = TRUE)

when I run it with 1.13 , it shows a unsued argument which did not show in version= 1.12

chuiqin commented 1 year ago

This error occurs because of an update to the AUCell version. The updated AUCell adds the splitByBlocks parameter. You can uninstall the AUCell package and then install the latest version of AUCell, which will solve this problem.

zy-199326 commented 1 year ago

thanks but which version fit ur package?1.14?

chuiqin commented 1 year ago

Just update the AUCell package instead of the irGSEA package.

zy-199326 commented 1 year ago

thanks，but why recently the score takes a longer time to get