problem about “category and method”

YMSWhuang commented 2 years ago

您好，很感谢能有这么一个整合好的R包直接使用，我有几个问题。1.irGSEA.score中的category = "H"，其中H是否可以修改为C2,C5等以便分析GO/KEGG通路，能提供一下应该如何修改？2.我看简书中提到了9种方法，包括AddModuleScore，Z-score等，后期是否因为需要考虑样本组成而被排除了，目前仅使用"AUCell", "UCell", "singscore", "ssgsea"4种方法，谢谢

zxkeeee commented 2 years ago

直接讲H改为你想要的基因集即可

chuiqin commented 2 years ago

First, you can use msigdbr::msigdbr_collections to view all available collections gene sets

> msigdbr::msigdbr_collections()
# A tibble: 23 × 3
   gs_cat gs_subcat         num_genesets
   <chr>  <chr>                    <int>
 1 C1     ""                         278
 2 C2     "CGP"                     3368
 3 C2     "CP"                        29
 4 C2     "CP:BIOCARTA"              292
 5 C2     "CP:KEGG"                  186
 6 C2     "CP:PID"                   196
 7 C2     "CP:REACTOME"             1604
 8 C2     "CP:WIKIPATHWAYS"          615
 9 C3     "MIR:MIR_Legacy"           221
10 C3     "MIR:MIRDB"               2377
# … with 13 more rows

If you want to use KEGG gene sets, you can do it:

pbmc3k.final <- irGSEA.score(object = pbmc3k.final, assay = "RNA", slot = "data", msigdb = T, species = "Homo sapiens", category = "C2", subcategory="CP:KEGG",geneid = "symbol", method = c("AUCell"), kcdf = 'Gaussian')

YMSWhuang commented 2 years ago

Thanks for your reply. I will try it :)

chuiqin / irGSEA

problem about “category and method” #7