episcanpy.ct.build_count_mtx¶

episcanpy.ct.build_count_mtx(cells, annotation, path='', output_file=None, writing_option='a', meth_context='CG', chromosome=['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '21', '22', '3', '4', '5', '6', '7', '8', '9', 'X', 'Y'], feature_names=None, threshold=1, ct_mtx=None, sparse=False)¶

Build methylation count matrix for a given annotation. It either write the count matrix (if given an output file) or return it as a variable (numpy matrix). If you want to add cells to an already existing matrix (with the same annotations), you put the initial matrix as ct_mtx or you specify the matrix to write + writing option = a

if you want to write down the matrix as a sparse matrix you have to specify it (not implented yet)

I need to pay attention to where I am writing the output file.

Also, verbosity..

Pay attention, it does not average variables. If you want to process many small features such as tfbs, we advise to use the dedicated function.

Parameters

cells: list of the file names to read to build the count matrix.
annotation: loaded annotation to use to build the count matrix ‘str’ or ‘list’ depending of the number of matrices to build
path: path to the input data.
output_file: name files to write. ‘str’ or ‘list’ depending of the number of matrices to build
writing_option: either ‘w’ if you want to erase potentialy already existing file or ‘a’ to append. ‘str’ or ‘list’ if you have a list of matrices and the writing options are differents
meth_context: read methylation in ‘CG’ of ‘CH’ context
chromosome: ‘MOUSE’ and ‘HUMAN’ (without mitochondrial genome) or list with chromosomes.
feature_names: If you want to write down the name of the annotation features. ‘Int’ (or ‘list’ if you have multiple annotations)
thereshold: the minimum of cytosines covered per annotation to calculate a methylation level. default=1 ‘Int’ (or ‘list’ if you have multiple annotations with different thresholds)
ct_mtx: numpy matrix containing the same set of annotations and for which you want to append. default: None
sparse: Boolean, writing option as a normal or sparse matrix. default: False