scGRN_getNt: scGRN_getNt

In mying4/scGRN: Gene Regulatory Network

Description

Get gene regulatory network

Usage

scGRN_getNt(df, gexpr, df_gene_id = 'hgnc_symbol', gexpr_gene_id = 'hgnc_symbol',
           cutoff_by = 'quantile', cutoff_percentage = 0.9,
           cutoff_absolute = 0.1,
           train_ratio = 0.7, num_cores = 2,
           mart = useMart(biomart="ENSEMBL_MART_ENSEMBL",
              dataset="hsapiens_gene_ensembl",
              host="uswest.ensembl.org"))

Arguments

df	a data.table got from function scGRN_getTF
gexpr	a data frame or large matrix. Each row represents one gene and each column represents one sample.
df_gene_id, gexpr_gene_id	the type of gene_id, in df and gexpr, should be 'hgnc_symbol' or 'ensembl_gene_id'.
cutoff_by	the type of cutoff criterion, should be 'quantile' or 'absolute'. If 'quantile' is specified, the cutoff_percentage will be used to pick the coefficients whose absolute value are larger that the quantile. Otherwise, cutoff_absolute will be used.
cutoff_percentage	a user defined numeric value to stop the cutoff specified as a proportion 0 to 1
cutoff_absolute	a user defined numeric value to stop the cutoff, defaults to 0.1
train_ratio	train size, should be between 0.0 and 1.0 and represent the proportion of the dataset to be included in the training set.
num_cores	number of cores used to do parallel computing
mart	a dataset in BioMart database

Value

a data frame containing TG, TF, promoter, enhancer and coef.

See Also

glmnet

Examples

data(gexpr)
data(TFs)
df <- scGRN_getNt(df = TFs, gexpr = gexpr,gexpr_gene_id = 'ensembl_gene_id')

mying4/scGRN documentation built on Aug. 11, 2020, 11:48 p.m.