Noi/NOTES/2012-3-24: Difference between revisions
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''' Link to calendar: [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]] ''' | ''' Link to calendar: [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]] ''' | ||
=== ASM analysis of UCLA SZ data set === | === ASM analysis of UCLA SZ data set === | ||
* Continued from http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-23 | * Continued from http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-23 | ||
* Plotting the distance between SNP-CpG showing ASM and -log10(p-value) | * Plotting the distance between SNP-CpG showing ASM and -log10(p-value) | ||
awk '{print $1"\t"$98}' UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt | sed s'/:/\t/g' | awk '{print $2-$3"\t"$4}' > UCLA_SZ_SeqDep_TTest-noSNP-SNP-CpG_distance_PVal0.05.txt | awk '{print $1"\t"$98}' UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt | sed s'/:/\t/g' | awk '{print $2-$3"\t"$4}' > UCLA_SZ_SeqDep_TTest-noSNP-SNP-CpG_distance_PVal0.05.txt | ||
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* In excel taking -log(p-value) and plot graph either absolute distance or distance between SNP-CpG | * In excel taking -log(p-value) and plot graph either absolute distance or distance between SNP-CpG | ||
[[File:SNP-CpG_distance-logp-val.png| 520px]] [[File:absSNP-CpG_distance-logp-val.png| 520px]] | [[File:SNP-CpG_distance-logp-val.png| 520px]] [[File:absSNP-CpG_distance-logp-val.png| 520px]] | ||
=== Discussion === | === Discussion === | ||
* Need to be filled in | * Need to be filled in |
Revision as of 22:57, 12 April 2012
Link to calendar: [[1]]
ASM analysis of UCLA SZ data set
- Continued from http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-23
- Plotting the distance between SNP-CpG showing ASM and -log10(p-value)
awk '{print $1"\t"$98}' UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt | sed s'/:/\t/g' | awk '{print $2-$3"\t"$4}' > UCLA_SZ_SeqDep_TTest-noSNP-SNP-CpG_distance_PVal0.05.txt Note: In UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt file, $2 = SNP position, $3 = CpG position, and $98 = p-value from T-test
- In excel taking -log(p-value) and plot graph either absolute distance or distance between SNP-CpG
File:SNP-CpG distance-logp-val.png File:AbsSNP-CpG distance-logp-val.png
Discussion
- Need to be filled in