Description Usage Arguments Value Examples
make signature object for ZSL (input for prediction)
1 2 3 | create_signature(Name, Tissue, w2v, Expr, Rowname, Cellname, cell_ontology,
Sdatatype, w2v_index = FALSE, Stopwords = stopwords,
Xdatatype = "scRNA-seq", R_output = FALSE, celltype_cnt_thr = TRUE)
|
Name |
user-defined name for the output |
Tissue |
tissue of the sample (please make sure the word of tissue must be same as pre-existing tissue list. If it is new tissue type, it doesn't matter)
|
w2v |
word2vector object
|
Expr |
expression/peak matrix (d <- make_input(input_var), d$norm_matrix) |
Rowname |
gene/peak_location of Expr (d<- make_input(input_var), d$rowname) |
Cellname |
cellname of Expr (d<- make_input(input_var), d$cellname) |
cell_ontology |
julia object of cell ontology (the result of make_cellontology) |
Sdatatype |
type of side-information (cell_ontology, ATAC-seq, or user-defined term) |
w2v_index |
TRUE if user needs to make side-information from cell ontology. FALSE if julia object of side-information exists |
Stopwords |
julia object of stopwords (the result of make_stopwords) |
Xdatatype |
type of Expr (scRNA-seq or scATAC-seq) |
R_output |
TRUE if the result of the function should be R object. FALSE if the result of the function should be julia object |
celltype_cnt_thr |
if the number for cell type exceeds, warning message will be sent and return FALSE. To ignore it, change the parameter into FALSE |
an attribute for ZSL (trained data) (julia object)
1 2 3 4 5 | d <- make_input(matrix, train = TRUE)
w2v <- make_w2v("Pubmed_index")
annot <- make_cellontology("cell ontology file")
stopwords <- make_stopwords(stopwords)
signature <- create_signature("user", "Heart", d$norm_matirx, d$rowname, d$cellname, annot, "cell_ontology", w2v_index = TRUE)
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