greatpy.tl.get_dist_to_tss

greatpy.tl.get_dist_to_tss(test, regdom)

Determine the distance from peaks to the transcription start site of the associated gene

Parameters:

test : str or pd.DataFrame: path of the file with the tests pics => columns: [“chr”,”chr_start”,”chr_end”]
regdom : str or pd.DataFrame: path of the file with the regulatory domains => columns: [“chr” “chr_start” “chr_end” “name” “tss” “strand”].

Returns:

res – dict with the distance from tss to the associated genes :

key = number of the input
value = distance from peaks to tss of associated genes

Return type:

dict

Examples

>>> test = pd.DataFrame(
    {
        "chr":["chr1"],
        "chr_start":[1052028],
        "chr_end": [1052049]}
    )
>>> regdom = pd.DataFrame(
    {
        "chr":["chr1","chr1"],
        "chr_start":[1034992,1079306],
        "chr_end": [1115089,1132016],
        "name":["RNF223","C1orf159"],
        "tss":[1074306,1116089],
        "strand":['-','-']
    })
>>> get_association(test,regdom)
...    {'RNF223':[-22278]}