scGRN_interaction: scGRN_interaction : find interaction from original data

In mying4/scGRN: Gene Regulatory Network

Description

Find enhancers and promoters for target genes.

Usage

scGRN_interaction(hic_interaction, enhancers, ref_promoters = 'all',up_stream = 2500,
down_stream = 2500, link_type = 'within' ,target_genes='all',gene_id_option = 'hgnc_symbol',
mart = useMart(biomart='ENSEMBL_MART_ENSEMBL',dataset='hsapiens_gene_ensembl',
host='uswest.ensembl.org'))

Arguments

hic_interaction	a data frame containing the variables : chr1,start1,end1,chr2,start2,end2 or chr,start1,end1,start2,end2. chr1,ch2 or chr should have the following format 'chrD'(D represents digit 1-22 or X Y) start1,end1,start2,end2 should be integer type.
enhancers	a data frame containing chr,start,end for enhancers.
ref_promoters	an optional data frame containing chr,start,end for promoters. If it is not supplied, promoters are from package - TxDb.Hsapiens.UCSC.hg19.knownGene. If it is supplied, ref_promoters are used and linked to target genes by package - TxDb.Hsapiens.UCSC.hg19.knownGene.
up_stream, down_stream	The up_stream and down_stream arguments define the number of nucleotides in the 5' and 3' direction, respectively. Used for annatating promoters.
link_type	"any", "start", "end" or "within" are used when ref_promoters is provided. Inherited from function GenomicRanges:findOverlapPairs.
target_genes	a vector of target genes which should be consistent with the gene_id_option.
gene_id_option	'hgnc_symbol' or 'ensembl_gene_id'.
mart	a dataset in BioMart database.

Details

it would be a good option to set a relavant large upstream and downstream and link the ref_promoters to genes by within the whole promoters we annotated.

Value

a data frame containing gene, gene_chr, promoter_start, promoter_end, enh_chr,enh_start,enh_end.

See Also

GenomicRanges,TxDb.Hsapiens.UCSC.hg19.knownGene,GenomicInteractions

Examples

data(enhancers)
data(hic_data)
df <- scGRN_interaction(hic_data,enhancers)

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