python/pymethylprocess/PreProcessDataTypes.py
def preprocess_enmix_pipeline(self, n_cores=6, pipeline='enmix', noob=False, qc_only=False, use_cache=False, bmiq=False):
        """Run complete ENmix or minfi preprocessing pipeline.

        Parameters
        ----------
        n_cores
            Number CPUs.
        pipeline
            Run enmix or minfi
        noob
            Noob norm or RAW if minfi running.
        qc_only
            Save and quit after only running QC?
        use_cache
            Load preexisting RGSet instead of running QC again."""
        cache_storage_path = os.path.join(self.idat_dir,'RGSet.rds')
        if use_cache:
            self.RGset=robjects.r('readRDS')(cache_storage_path)
        else:
            self.load_idats()
        if qc_only:
            robjects.r('saveRDS')(self.RGset,cache_storage_path)
            exit()
        if not os.path.exists(cache_storage_path):
            robjects.r('saveRDS')(self.RGset,cache_storage_path)
        if pipeline =='enmix':
            self.preprocessENmix(n_cores)
        else:
            if noob:
                self.preprocessNoob()
            else:
                self.preprocessRAW()
        self.return_beta()
        if bmiq:
            self.get_beta(bmiq = True, n_cores=n_cores)
        else:
            self.get_beta()
        self.filter_beta()
        self.extract_pheno_data(methylset=True)
        return self.pheno, self.beta_final
Run complete ENmix or minfi preprocessing pipeline.

        Parameters
        ----------
        n_cores
            Number CPUs.
        pipeline
            Run enmix or minfi
        noob
            Noob norm or RAW if minfi running.
        qc_only
            Save and quit after only running QC?
        use_cache
            Load preexisting RGSet instead of running QC again.
Run complete ENmix or minfi preprocessing pipeline.
Parameters


Run complete ENmix or minfi preprocessing pipeline . Parameters
def preprocess_enmix_pipeline(self, n_cores=6, pipeline='enmix', noob=False, qc_only=False, use_cache=False, bmiq=False):
        cache_storage_path = os.path.join(self.idat_dir,'RGSet.rds')
        if use_cache:
            self.RGset=robjects.r('readRDS')(cache_storage_path)
        else:
            self.load_idats()
        if qc_only:
            robjects.r('saveRDS')(self.RGset,cache_storage_path)
            exit()
        if not os.path.exists(cache_storage_path):
            robjects.r('saveRDS')(self.RGset,cache_storage_path)
        if pipeline =='enmix':
            self.preprocessENmix(n_cores)
        else:
            if noob:
                self.preprocessNoob()
            else:
                self.preprocessRAW()
        self.return_beta()
        if bmiq:
            self.get_beta(bmiq = True, n_cores=n_cores)
        else:
            self.get_beta()
        self.filter_beta()
        self.extract_pheno_data(methylset=True)
        return self.pheno, self.beta_final
def preprocess_enmix_pipeline ( self , n_cores = 6 , pipeline = 'enmix' , noob = False , qc_only = False , use_cache = False , bmiq = False ) : cache_storage_path = os . path . join ( self . idat_dir , 'RGSet.rds' ) if use_cache : self . RGset = robjects . r ( 'readRDS' ) ( cache_storage_path ) else : self . load_idats ( ) if qc_only : robjects . r ( 'saveRDS' ) ( self . RGset , cache_storage_path ) exit ( ) if not os . path . exists ( cache_storage_path ) : robjects . r ( 'saveRDS' ) ( self . RGset , cache_storage_path ) if pipeline == 'enmix' : self . preprocessENmix ( n_cores ) else : if noob : self . preprocessNoob ( ) else : self . preprocessRAW ( ) self . return_beta ( ) if bmiq : self . get_beta ( bmiq = True , n_cores = n_cores ) else : self . get_beta ( ) self . filter_beta ( ) self . extract_pheno_data ( methylset = True ) return self . pheno , self . beta_final
Run complete ENmix or minfi preprocessing pipeline.
Run complete ENmix or minfi preprocessing pipeline .
"""Run complete ENmix or minfi preprocessing pipeline.

        Parameters
        ----------
        n_cores
            Number CPUs.
        pipeline
            Run enmix or minfi
        noob
            Noob norm or RAW if minfi running.
        qc_only
            Save and quit after only running QC?
        use_cache
            Load preexisting RGSet instead of running QC again."""
self
n_cores
pipeline
noob
qc_only
use_cache
bmiq