scGRN_getTF: scGRN_getTF

In mying4/scGRN: Gene Regulatory Network

Description

Find transcription factors which bind to promoters and enhancers

Usage

scGRN_getTF(df, database = JASPAR2018, species_type = 9606, min_score = 0.9,
                   pwm_type = 'prob',num_cores = 2)

Arguments

df	a data frame which can from the output of function scGRN_interation or available interation data. The data frame should contain gene, gene_chr, promoter_start, promoter_end,
database	a database of transcription factor binding profiles which can be searched by TFBSTools.
species_type	defaults to 9606, which represents human.
min_score	quantile set to find the potential TFs for a given region, defaults to 0.9.
num_cores	number of cores used to do parallel computing, speeding up the match process.
pwm_tpye	the type of PWM generated, should be one of "log2probratio" or "prob". "log2probratio" will generate the PWM matrix in log-scale, while "prob" will give the PWM matrix in probability scale of 0 to 1. Inherited from toPWM function.

Value

a data.table containing gene, promoter, enhancer, promoter_TF, enhancer_TF. The type of elements in promoter_TF and enhancer_TF is list.

See Also

JASPAR2018, TFBSTools

Examples

data(interaction_data)
df <- scGRN_getTF(interaction_data)

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