n_fold_logistic: Title

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

Description

Description

Usage

n_fold_logistic(tm_facs, Gene_usage, s, annot, mincell, Ngene, data_name,
  sdatatype, fdrthr = 0.1, n = 5, k = 1, tissue_opt = FALSE,
  Celltype_specific = FALSE, ncore = 1)

Arguments

tm_facs

result of import_tm_facs

Value

att_set, meta_set, logistic_result

• att_set: attribute_set

• meta_set: result of logistic regression (same as create_meta_index_av)

• logistic_result: result of logistic regression prediction (same a leave_one_val)

• n_fold: all the results needs n-fold index (ex: res$att_set$1_fold: att_set)

Examples

tm_facs <- input_tm_facs("address")
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)
res <- n_fold_logistic(tm_facs, 2048, side_info, cell_ontology, FALSE, 64, "user", "cell_ontology")

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