Process Module

Process module is the main module of SCMeTA. It provides a set of tools for single-cell metabolism time-course analysis, including data loading, full path of process (preprocess, main-process, past-process). SCMeTA is designed to be easy to use and easy to extend. It is built on top of the pandas and numpy.

The main process pipeline of SCMeTA is shown below:

from SCMeTA import Process

# Initialize a Process object, refer_mz is the characteristic metabolite for finding the cells.

sc = Process(refer_mz=760.58)

# Load data, path can be a dir path or a file path.

sc.load(path = 'data.RAW')

# Pre-process data

sc.pre_process(resolution: float = 0.01, count: int = 10)


# Process single-cell metabolism data.

sc.process(
    max_ratio: float = 0.1
    adjacent: int = 3,
    snr: float = 3,
    resolution: float = 0.1,
    threshold: float = 0.2,
    lock_mz: bool = False,
    filter_method: str = "all"
)

# Post-process data

data: dict[name, SCData] = sc.post_process(
    normalize_method=["log", "zscore"]
    fillna_method: str = "none",
)

# Save results

sc.save()