Description Usage Arguments Value Examples
predict cell type with logistic regression model
1 2 3 | logistic_prediction_cell(iscell, meta_model_list, query,
gn_overlap_thr = 0.5, logistic_thr = 0.5, tissue_opt = FALSE,
celltype_specific = FALSE)
|
iscell |
attribute set |
meta_model_list |
result from create_meta_index |
query |
signature object of query |
gn_overlap_thr |
minimum gene overlap ratio of attribute in attribute set between query data |
logistic_thr |
threshold for each cell whether predicted score from logistic regression model is confident |
tissue_opt |
TRUE if user wants to find tissue-origin |
celltype_specific |
TRUE if user wants to calculate the weight fo each tissue with only matched cell type. Otherwise, weight for each tissue will be calculated with whole celltypes (default: FALSE; tissue_opt should be TRUE to use this parameter) |
return 2 confusion matrix
confusion: a confusion matrix of prediction result
all_confusion: a confusion matrix of prediction result in each cell
1 2 3 | meta_model <- create_meta_index_av(att_set, sig_set)
res_list <- logistic_prediction_cell(att_set, meta_model, query_signature)
res_list$confusion or res_list$all_confusion
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