error in cell chat when trying to identifyoverexpressedgenes

[teganmct]

Dear Professor Jin,

An amazing package! I have a query regarding cellchat. i am coming across an error when I try to run the function identifyoverexpressedgenes in cellchat and I would be hugely grateful for your help trying to resolve this. > cellchatPSA <- identifyOverExpressedGenes(cellchatPSA)
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Error in (function (cl, name, valueClass) :
assignment of an object of class "character" is not valid for @'var.features' in an object of class "CellChat"; is(value, "list") is not TRUE
3.
stop(gettextf("assignment of an object of class %s is not valid for @%s in an object of class %s; is(value, "%s") is not TRUE",
dQuote(valueClass), sQuote(name), dQuote(cl), slotClass),
domain = NA)
2.
(function (cl, name, valueClass)
{
ClassDef <- getClass(cl)
slotClass <- ClassDef@slots[[name]] ...
1.
identifyOverExpressedGenes(cellchatPSA)

below is my code:#part 1 create a cell chta object from a seurat object ####
Idents(noabseq) <- "Sample_Name"
seurat_objectHC <- subset(noabseq, idents = "HC")
seurat_objectPSA <- subset(noabseq, idents = "PSA")

Idents(seurat_objectHC) <- "celltypes"
data.inputHC <- GetAssayData(JoinLayers(seurat_objectHC, assay ="RNA", slot = "data"))
labelsHC <- Idents(seurat_objectHC)
metaHC <- data.frame(group = labelsHC, row.names = names(labelsHC))
cellchatHC <- createCellChat(object = data.inputHC, meta = metaHC, group.by = "group")

Idents(seurat_objectPSA) <- "celltypes"
data.inputPSA <- GetAssayData(JoinLayers(seurat_objectPSA, assay ="RNA", slot = "data"))
labelsPSA <- Idents(seurat_objectPSA)
metaPSA <- data.frame(group = labelsPSA, row.names = names(labelsPSA))
cellchatPSA <- createCellChat(object = data.inputPSA, meta = metaPSA, group.by = "group")

#part 2 cell chat databases cellchatdb ####
CellChatDB <- CellChatDB.human
showDatabaseCategory(CellChatDB.human)
#show structure of databases
dplyr::glimpse(CellChatDB$interaction)

#set all cellchat db for cell-cell communications
CellChatDB.use <- CellChatDB.human

#set a subset of cellchat db for cell-cell communication analysis if required
#CellChatDB.use <- subsetDB(CellChatDB.human, search = "secreted Signaling")
#CellChatDB.use <- subsetDB(CellChatDB.human, search = "ECM-Receptor")
#CellChatDB.use <- subsetDB(CellChatDB.human, search = "Cell-Cell Contact")

tutorial showing how to download complex, cofactor, gene info and interaction a

not shown here on youtube

#PART 3 inference of cell-cell communication network analysis
library(CellChat)
library(patchwork)
library(circlize)
options(stringsAsFactors = FALSE)

cellchatHC@DB <- CellChatDB.use
cellchatPSA@DB <- CellChatDB.use

#set the full human ligand-receptor interaction database
cellchatHC<-subsetData(cellchatHC)
cellchatPSA<-subsetData(cellchatPSA)

#not working coming up with an error
cellchatHC <- identifyOverExpressedGenes(cellchatHC)
cellchatHC <- identifyOverExpressedInteractions(cellchatHC)

cellchatPSA <- identifyOverExpressedGenes(cellchatPSA)
cellchatPSA <- identifyOverExpressedInteractions(cellchatPSA)

Hopefully your expert insight will be able to help solve this. Thankyou in advance.

Tegan