create_signature: create_signature

In hemberg-lab/sctransfermap: sctransfermap for predicting cell type in single-cell data (RNA-seq and ATAC-seq)

Description

make signature object for ZSL (input for prediction)

Usage

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)

Arguments

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) Mouse: Aorta, Brain, Diaphragm, Fat, Heart, Kidney, LargeIntestine, LimbMuscle, Liver, Lung, MammaryGland, Marrow, Pancreas, Skin, Spleen, Thymus, Tongue, Trachea
w2v	word2vector object output of make_w2v pre-existing side-information object (julia object) (ex: julia_obj$side_information) output of generate_sideinformation
Expr	expression/peak matrix (d <- make_input(input_var), d$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

Value

an attribute for ZSL (trained data) (julia object)

Examples

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)

hemberg-lab/sctransfermap documentation built on Nov. 11, 2019, 6:23 a.m.