episcanpy.ct.load_features

episcanpy.ct.load_features(file_features, chromosomes=['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '21', '22', '3', '4', '5', '6', '7', '8', '9', 'X', 'Y'], path='', sort=False)

The function load features is here to transform a bed file into a usable set of units to measure methylation levels. It has to be a bed-like file. You also need to specify the chromosomes you use as a list of characteres like [‘1’, ‘7’, ‘8’, ‘9’, ‘X’, ‘Y’, ‘M’]. The chromosome list you give as input can be not ordered. If you don’t specify the chromosomes, the default is the human genome (including X, Y and mitochondrial DNA). THE BED FILE need to be sorted !! (Maybe I should add an option to sort the file).

The output is a dictionary where the keys are chromosomes and the value is a list containing [start, end, name] for every feature extracted.

Parameters

file_features

the names of the bed file you want to load.

chromosomes

chromosomes corresponding to the bed file. If not specified, it’s human by default

path

if you want to specify the path where your bed file is.

sort

if True, the bed file is sorted based on starting coordinates.