Estimate the cell fraction of cell lineages and sub lineages.
Usage
SpaCET.deconvolution(
SpaCET_obj,
cancerType,
signatureType = NULL,
adjacentNormal = FALSE,
coreNo = 6
)Arguments
- SpaCET_obj
A SpaCET object.
- cancerType
Cancer type of the current tumor ST dataset.
- signatureType
Indicate the tumor signature type, NULL, CNA, expr, or seq_depth. Default: NULL (automatically detect CNA or expr).
- adjacentNormal
Indicate whether your sample is normal tissue adjacent to the tumor. If TURE, SpaCET will skip the stage of malignant cell inference. Default: FALSE.
- coreNo
Core number in parallel computation.