what's the mean of direction

[haowBio]

Hi, I want to know the mean of irGSEA.integrate result, the column "direction" which have two levels, how can you define up or down? Is it compare to median of the score

[haowBio]

Because there are multiple cell types, I want to know how these compare

[chuiqin]

For example, it suggests the mean of enrichment scores of cluster B lower than the remaining clusters (except the cluster B) when the direction is down. If you are familiar with the Seurat package, you can easy to repeat it as follow:

pbmc3k.final <- SeuratObject::UpdateSeuratObject(pbmc3k.final)
# Seurat object
pbmc3k.final <- irGSEA.score(object = pbmc3k.final, assay = "RNA", slot = "data", msigdb = T, species = "Homo sapiens",
category = "H", geneid = "symbol", method = c("AUCell", "UCell", "singscore", "ssgsea"), kcdf = 'Gaussian')
# Integrated analysis
result.dge <- irGSEA.integrate(object = pbmc3k.final, group.by = "seurat_annotations", metadata = NULL, col.name = NULL,
method = c("AUCell","UCell","singscore","ssgsea"))
head(result.dge$AUCell, 1)
#                   Name         p_val    avg_diff     p_val_adj cluster direction
# 1 HALLMARK-ANGIOGENESIS 2.364593e-106 -0.05079023 1.182296e-104       B      down
#  methods
# 1  AUCell

pbmc3k.final <- SeuratObject::UpdateSeuratObject(pbmc3k.final)
# Seurat object
pbmc3k.final <- irGSEA.score(object = pbmc3k.final, assay = "RNA", slot = "data", msigdb = T, species = "Homo sapiens",
category = "H", geneid = "symbol", method = c("AUCell", "UCell", "singscore", "ssgsea"), kcdf = 'Gaussian')
result.dge2 <- Seurat::FindMarkers(object = pbmc3k.final,
                         assay = "AUCell",
                         slot = "scale.data",
                         ident.1 = "B",
                         ident.2 = NULL,
                         test.use = "wilcox",
                         min.pct = -Inf,
                         logfc.threshold = 0,
                         min.cells.group = 0,
                         min.diff.pct = -Inf,
                         verbose = F, group.by = "seurat_annotations",
                         min.cells.feature = 0)
result.dge2 <- result.dge2 %>% tibble::rownames_to_column(var = "gene") %>%
    dplyr::mutate(cluster = "B", direction = dplyr::if_else(avg_diff >0, "up", "down")) %>%
    dplyr::select(-c("pct.1", "pct.2"))
head(result.dge2 ,1)
#                   gene         p_val    avg_diff     p_val_adj cluster direction
# 1 HALLMARK-ANGIOGENESIS 2.364593e-106 -0.05079023 1.182296e-104       B      down

The column direction is related to the column avg_diff.

[haowBio]

Thank you for you reply The result is the same as I expected. It's a very nice tool. Can irGSEA have the same function with Seurat::FindMarkers, which can specify ident1 and ident2, so that I can compare in two groups which I wanted.

[chuiqin]

Sorry, this function is not supported in the current version. But the function will be added in next version.

[haowBio]

Thank you, Looking forward to the next version