fieldnanax.blogg.se - Math illustrations silent install

n is chosen based on the above two steps. extractSignatures - uses non-negative matrix factorization to decompose the matrix into n signatures.

Best possible signature is the value at which Cophenetic correlation drops significantly.

plotCophenetic - which draws an elblow plot and helps you to decide optimal number of signatures.

estimateSignatures - which runs NMF on a range of values and measures the goodness of fit - in terms of Cophenetic correlation.

Signature analysis includes following steps. # Hugo_Symbol Enriched nonEnriched pval or ci.up PlotApobecDiff( tnm = laml.tnm, maf = laml, pVal = 0.2) # -Processing clinical data There is also a small function - plotEnrichmentResults which can be used to plot these results. One can use any sort of clincial feature to perform such an analysis. These are well known results and this function effectively recaptures them. Similarly DNMT3A is in M5, RUNX1 is in M0, and so on. # 8: 0.133827 0.003146708 0.8848897 0.5880102Ībove results shows IDH1 mutations are enriched in M1 subtype of leukemia compared to rest of the cohort. Significant associations p-value < 0.05 fab.ce $groupwise_comparision # Hugo_Symbol Group1 Group2 n_mutated_group1 n_mutated_group2 p_value

# Hugo_Symbol Primary Relapse pval or ci.up ci.low pt.vs.rt <- mafCompare( m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary', m2Name = 'Relapse', minMut = 5) print(pt.vs.rt) # $results #Considering only genes which are mutated in at-least in 5 samples in one of the cohort to avoid bias due to genes mutated in single sample. We can plot the results using plotOncodrive. # AlteredSamples clusters muts_in_clusters clusterScores protLen zscore # Missense_Mutation Nonsense_Mutation Splice_Site total MutatedSamples Head(laml.sig) # Hugo_Symbol Frame_Shift_Del Frame_Shift_Ins In_Frame_Del In_Frame_Ins # gene1 gene2 pValue oddsRatio 00 11 01 10 Event somaticInteractions( maf = laml, top = 25, pvalue = c( 0.05, 0.1)) #exclusive/co-occurance event analysis on top 10 mutated genes.