Noi/NOTES/2012-3-24: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Noi
No edit summary
>Noi
Line 1: Line 1:
''' 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#mpo_and_mQTL_analysis_.28have_been_repeated_on_2012_03_26.29
* 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
Line 7: Line 7:
* 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

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