"Step 2. CCC" Error in do.call(rbind, ccc_list) : second argument must be a list

[bianjh-cloud]

Hi SecAct Developers,

Thank you for providing this tool. When I am running the infer Cell-Cell Communication step, I am getting the following error:

SpaCET_obj <- SecAct.CCC.scST(

• SpaCET_obj,
• cellType_meta = "cellType",
• scale.factor = 1000,
• radius = 20,
• ratio_cutoff = 0.2,
• padj_cutoff = 0.01
• )
  [1] "Step 1. Filtering"
  [1] "31/48 secreted proteins are kept to infer cell-cell communication."
  [1] "Step 2. CCC"
  Error in do.call(rbind, ccc_list) : second argument must be a list

After going through the function line by line, I think this error is caused by the following line:

cellTypePair <- cellTypePair[cellTypePair1 > cellTypePair2,
]

which generated NAs that cause the downstream compute_pair() and cbind() steps to fail. My workaround is the following, if it might be helpful:

cellTypePair <- cellTypePair[cellTypePair[,"cellTypePair1"] > cellTypePair[,"cellTypePair2"], ]

[beibeiru]

Hi, @bianjh-cloud ,

Thank you for your interest in our SecAct package.
Would you please share your SpaCET_obj with me? I will fix it soon.

Best,
Beibei