Build functions for the module qc_filter.py
Below is described the functions to be designed for the module qc_filter.py, which will work on QC and filtering the data. This module is in directory sctoolbox, at the dev branch.
def cell_mitochondrial():
'''
Filter cells based on the mitochondrial content.
Exclude >= cutoff
Default cutoff: automatic cutoff from from distribution analysis
Custom cutoff: user define the cutoff
Return anndata
'''
def cell_numgenes():
'''
Filter cells based on the number of genes.
Exclude <= cutoff
Default cutoff: automatic cutoff from from distribution analysis
Custom cutoff: user define the cutoff
Return anndata
'''
def genes_mitochondrial():
'''
Filter mitochondrial genes based on a custom list of genes defined by the co-worker.
Exclude based on the custom list.
Return anndata
'''
def genes_genderspecific():
'''
Filter gender-specific genes based on a custom list of genes defined by the co-worker.
Exclude based on the custom list.
Return anndata
'''
def genes_others():
'''
Filter other genes based on a custom list of genes defined by the co-worker.
Exclude based on the custom list.
Return anndata
'''
def genes_mincells():
'''
Filter genes expressed in few cells.
Exclude <= cutoff
Default cutoff: automatic cutoff from from distribution analysis
Custom cutoff: user define the cutoff
Return anndata
'''
Edited by guilherme.valente