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===Round 1: MHL in imputed,normalized merge data which prediction analysis missed === *1, Find out regions that contain HMHs in primary tumor but not in N37 normal tissues or normal plasma. scp shg047@genome-miner.ucsd.edu:/home/kunzhang/CpgMIP/MONOD/Data/ cat PC-P-*.methHapCounts.txt | ../scripts/get_tumor_specific_HMH_regions.pl N37_ten_tissues_NC-P-ALL_RRBS-dRRBS.methHapCounts.txt > PC-P_N37_plasma_specific_HMH_regions.bed & cat 7-P-*.methHapCounts.txt | ../scripts/get_tumor_specific_HMH_regions.pl N37_ten_tissues_NC-P-ALL_RRBS-dRRBS.methHapCounts.txt > LC-P_N37_plasma_specific_HMH_regions.bed & cat 6-P-*.methHapCounts.txt | ../scripts/get_tumor_specific_HMH_regions.pl N37_ten_tissues_NC-P-ALL_RRBS-dRRBS.methHapCounts.txt > CRC-P_N37_plasma_specific_HMH_regions.bed & samtools view -H 6-P-10.sorted.clipped.bam > header.sam samtools merge -h header.sam 6-P-10.sorted.clipped.bam 6-P-1.sorted.clipped.bam 6-P-2.sorted.clipped.bam 6-P-3.sorted.clipped.bam 6-P-4.sorted.clipped.bam 6-P-5.sorted.clipped.bam 6-P-6.sorted.clipped.bam 6-P-7.sorted.clipped.bam 6-P-8.sorted.clipped.bam 6-P-9.sorted.clipped.bam *1,define clean genomic region in normal plasma (low methylation region) 704 haplotype regions were identified as the cancer specific(solid tissue) and were clean in the normal plasma samples. [[File:Figure 4D.txt]] *2 Calculate the cumulation/average MHL for these region (tumor specific) for a plasma sample. ** MHL distribution for above defined regions [[File:7AB3.tm.png|400px]] *** CP: cancer plasma, CT: cancer tissue, NP: normal plasma *3. assign a probability for the plasma is belong to 'cancer' or 'normal' as well as which tissue-of-origin? ** [[merge cancer tissue, cancer plamsa and normal plasma haploinfo files]] <nowiki> Colon: 740 > myData type mean sd n sem me 1 CP 0.303570259 0.04889567 740 0.0184808266 2.149566e+00 2 NP 0.001489827 0.00036459 740 0.0001378021 9.520868e+11 3 TP 0.004369450 0.01452305 740 0.0054891956 2.759810e+00 </nowiki> <nowiki> Lung: 740 > myData type mean sd n sem me 1 CP 0.310171625 0.05194363 740 0.0196328452 2.137493e+00 2 NP 0.001489827 0.00036459 740 0.0001378021 9.520868e+11 3 TP 0.008964632 0.02154434 740 0.0081429953 2.444373e+00 </nowiki>
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