make_tm_facs_attribute_set: make_tm_facs_attribute_set

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

Description

creating attribute set from the result of make_input_tm_facs

Usage

make_tm_facs_attribute_set(tm_facs_input, s, annot, mincell, data_name,
  sdatatype, ngene = 64, fdrthr = 0.1, lambda = 1, gamma = 1)

Arguments

tm_facs_input	the result of make_input_tm_facs
s	side-information (jula object)
annot	cell ontology (julia object)
mincell	TRUE if user wants to give minimum cell type thresholding
data_name	name for the attribute
sdatatype	type of side-information (cell_ontology, ATAC-seq, or user-defined term)
ngene	a number of vector size after JL transformation
fdrthr	fdr threshold for calculating similarity score during training
lambda	parameter for ZSL
gamma	paramter for ZSL

Value

attribute set

Examples

tm_facs_input <- make_input_tm_facs(tm_facs)
w2v <- make_w2v("Pubmed.index")
cell_ontology <- make_cellontology("cell_ontogloy_file")
stopword <- make_stopwords(stopwords)
side_info <- make_w2v_sideinfo(w2v, cell_ontology, stopword)
sig_set <- make_tm_facs_attribute_set(tm_facs_input, side_info, cell_ontology, FALSE, "user", "cell_ontology")

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