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chuiqin / irGSEA

The integration of single cell rank-based gene set enrichment analysis
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Error when calculate irGSEA.score using category = "C5", subcategory = "GO:BP" parameter #18

Open itolov opened 1 year ago

itolov commented 1 year ago

hi developer, thank you so much for your helpful tools. I tried to use irGSEA to calculate the GO -BP geneset enrichment scores. But when I calculated the enrichment score as shown below: skin.GO.BP <- irGSEA.score(object = skin.combined, assay = "RNA", slot = "data", seeds = 123, ncores = 1, min.cells = 3, min.feature = 0, custom = F, geneset = NULL, msigdb = T, species = "Mus musculus", category = "C5", subcategory = "GO:BP", geneid = "symbol", method = c("AUCell", "UCell", "singscore", "ssgsea"), aucell.MaxRank = NULL, ucell.MaxRank = NULL, kcdf = 'Gaussian') the reaction was:

Error in calculate_Uscore(m, features = features, maxRank = maxRank, chunk.size = chunk.size, : One or more signatures contain more genes than maxRank parameter. Increase maxRank parameter or make shorter signatures Traceback:

  1. irGSEA.score(object = skin.combined, assay = "RNA", slot = "data", . seeds = 123, ncores = 1, min.cells = 3, min.feature = 0, . custom = F, geneset = NULL, msigdb = T, species = "Mus musculus", . category = "C5", subcategory = "BP", geneid = "symbol", method = c("AUCell", . "UCell", "singscore", "ssgsea"), aucell.MaxRank = NULL, . ucell.MaxRank = NULL, kcdf = "Gaussian")
  2. UCell::ScoreSignatures_UCell(matrix = my.matrix, features = h.gsets.list, . maxRank = ucell.MaxRank, w_neg = 1, ncores = ncores, force.gc = T)
  3. calculate_Uscore(m, features = features, maxRank = maxRank, chunk.size = chunk.size, . w_neg = w_neg, ties.method = ties.method, ncores = ncores, . BPPARAM = BPPARAM, force.gc = force.gc, name = name)
  4. stop("One or more signatures contain more genes than maxRank parameter.\n Increase maxRank parameter or make shorter signatures")

I am confused because I used a similar code to get the hallmark and KEGG results. Could you give me any suggestions? Or does anyone have an idea as to why this occurs?

sherryshen2020 commented 1 year ago

ucell.MaxRank Maximum number of genes to rank per cell. Above this rank, a given gene is considered as not expressed. Default 1500 when it set to NULL. You can input special number, such as 2000, to increase the rank range. The parameter works if "UCell" is selected in "method".