Complete workflow to create base GRN from scATAC-seq peaks.
Usage
create_base_grn(
peaks_df,
ref_genome,
motifs = NULL,
upstream = 2000,
downstream = 2000,
fpr = 0.02,
min_peaks = 10,
n_cores = 1
)
Arguments
- peaks_df
Data frame with chr, start, end columns
- ref_genome
Reference genome
- motifs
Motif database (NULL for JASPAR)
- upstream
TSS upstream distance
- downstream
TSS downstream distance
- fpr
Motif scanning FPR
- min_peaks
Minimum peaks for TF filtering
- n_cores
Number of parallel cores
Value
TFdict suitable for Oracle$import_TF_data()