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=== Pearson's Chi-square test === * We need to filter for locus where blood is significantly different from cancer but not signficantly different from blood. * Use the Chi-Square test of independence (Pearson's Chi square) to compare pairwise between blood and each cancer type. Output only the locus count for blood where the locus count is dependent on the sample type (reject the null hypothesis). * Perl script : [[File:chisqIndep_cgLocusAlleles.txt]] chiSqIndep_cgLocusAlleles [cgLocusAlleles file A] [cgLocusAlleles file b] * Example ChiSqIndep for Locus: chr6:392409:392417:392428:392435 (between Blood_B1 and PANC1) Rows: 2 Columns: 9 Degree of Freedom: 8 Total Count: 136 Chi-square Statistic: 136 p-value: 0.00000000000000000000000016093 Warning: some of the cell counts might be too low. UUUU UUUM UUMM UMMM MUUU MUUM MUMM MMUM MMMM rtotal Blood 30 0 0 0 0 0 0 0 0 30 (6.62) (0.88) (0.66) (0.22) (0.44) (2.65) (2.87) (0.66) (15.00) PANC1 0 4 3 1 2 12 13 3 68 106 (23.38) (3.12) (2.34) (0.78) (1.56) (9.35) (10.13) (2.34) (53.00) ctotal 30 4 3 1 2 12 13 3 68 136 * Example ChiSqIndep for Locus: chr5:1887153:1887159:1887179:1887185 (between Blood_B1 and Blood_H11) Rows: 2 Columns: 10 Degree of Freedom: 9 Total Count: 437 Chi-square Statistic: 24.8046419350707 p-value: 0.0031951 Warning: some of the cell counts might be too low. UUUU UUUM UUMU UUMM UMUU UMUM UMMM MUUU MUMM MMUM rtotal B1 350 2 2 1 2 0 0 2 1 2 362 (345.43) (4.14) (2.49) (1.66) (1.66) (0.83) (1.66) (1.66) (0.83) (1.66) H11 67 3 1 1 0 1 2 0 0 0 75 (71.57) (0.86) (0.51) (0.34) (0.34) (0.17) (0.34) (0.34) (0.17) (0.34) ctotal 417 5 3 2 2 1 2 2 1 2 437 * Summary count of sample-dependent locus, using Blood_B1 as representative blood profile against Blood_H11 and Blood_D1 2162 Blood_B1.1.cgLocusAlleles.indepVersus.Blood_D1.1.cgLocusAlleles 1435 Blood_B1.1.cgLocusAlleles.indepVersus.Blood_H11.1.cgLocusAlleles * Summary count of sample-dependent locus, Blood_B1 versus cancer haplotypes 8724 Blood_B1.1.cgLocusAlleles.indepVersus.BE2C_1.1.cgLocusAlleles 11462 Blood_B1.1.cgLocusAlleles.indepVersus.BXPC3_1.1.cgLocusAlleles 10516 Blood_B1.1.cgLocusAlleles.indepVersus.PANC1_1.1.cgLocusAlleles 11428 Blood_B1.1.cgLocusAlleles.indepVersus.T98G_1.1.cgLocusAlleles 11020 Blood_B1.1.cgLocusAlleles.indepVersus.U87MG_1.1.cgLocusAlleles * Generate a final file combining all unique sample-locus dependent locus, then remove any dependent locus between Blood_B1 and other blood profiles. 10738 Blood_Indep_All.cgLocusAlleles
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