def merge(self,rmout): for rawspectrum in self.rt_all.keys(): for peptide in self.rt_all[rawspectrum]: rt = [] for idx in all_indices(sorted(self.prob_all[rawspectrum][peptide], reverse=True)[0],self.prob_all[rawspectrum][peptide]): rt.append(self.rt_all[rawspectrum][peptide][idx]) if rmout and len(rt) > 2: self.rt[rawspectrum][peptide] = lmedian(array(rt)[chauvenet(array(rt),array(rt))]) self.rt_run[rawspectrum][peptide] = array(rt)[chauvenet(array(rt),array(rt))] else: self.rt[rawspectrum][peptide] = lmedian(rt) self.rt_run[rawspectrum][peptide] = rt
def merge(self,rmout): for rawspectrum in self.rt_all: for peptide in self.rt_all[rawspectrum]: rt = [] for idx in all_indices(sorted(self.prob_all[rawspectrum][peptide], reverse=True)[0],self.prob_all[rawspectrum][peptide]): rt.append(self.rt_all[rawspectrum][peptide][idx]) if rmout and len(rt) > 2: self.rt[rawspectrum][peptide] = lmedian(array(rt)[chauvenet(array(rt),array(rt))]) self.rt_run[rawspectrum][peptide] = array(rt)[chauvenet(array(rt),array(rt))] else: self.rt[rawspectrum][peptide] = lmedian(rt) self.rt_run[rawspectrum][peptide] = rt
def transform(self, rmout): irt = {} for rawspectrum in self.rt: for peptide in self.rt[rawspectrum]: self.irt[rawspectrum][peptide] = scipy.polyval( [self.a[rawspectrum], self.b[rawspectrum]], self.rt[rawspectrum][peptide]) if peptide not in irt: irt[peptide] = [] irt[peptide].append(self.irt[rawspectrum][peptide]) for peptide in irt: if len(irt) == 1: self.irt_merged[peptide] = round(irt[peptide][0], 5) else: if rmout and len(irt) > 2: self.irt_merged[peptide] = round( lmedian( array(irt[peptide])[invert( chauvenet(array(irt[peptide]), array(irt[peptide])))]), 5) else: self.irt_merged[peptide] = round(lmedian(irt[peptide]), 5) for i in range(0, len(self.blocks)): self.blocks[i].replace(self.irt_merged[self.blocks[i].peptide])
def transform(self,rmout): irt = {} for rawspectrum in self.rt.keys(): for peptide in self.rt[rawspectrum].keys(): self.irt[rawspectrum][peptide] = scipy.polyval([self.a[rawspectrum],self.b[rawspectrum]],self.rt[rawspectrum][peptide]) if peptide not in irt.keys(): irt[peptide] = [] irt[peptide].append(self.irt[rawspectrum][peptide]) for peptide in irt.keys(): if len(irt) == 1: self.irt_merged[peptide] = round(irt[peptide][0],5) else: if rmout and len(irt) > 2: self.irt_merged[peptide] = round(lmedian(array(irt[peptide])[invert(chauvenet(array(irt[peptide]),array(irt[peptide])))]),5) else: self.irt_merged[peptide] = round(lmedian(irt[peptide]),5) for i in range(0,len(self.blocks)): self.blocks[i].replace(self.irt_merged[self.blocks[i].peptide])