http://statgen.us/index.php?action=history&feed=atom&title=Genome-wide_Association-Quality_Control_Exercise
Genome-wide Association-Quality Control Exercise - Revision history
2026-04-05T18:20:00Z
Revision history for this page on the wiki
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http://statgen.us/index.php?title=Genome-wide_Association-Quality_Control_Exercise&diff=750&oldid=prev
Serveradmin at 18:07, 24 January 2019
2019-01-24T18:07:15Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 18:07, 24 January 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28" >Line 28:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  plink --file GWAS_clean2 --remove IBS_excluded.txt --recode --out GWAS_clean3</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  plink --file GWAS_clean2 --remove IBS_excluded.txt --recode --out GWAS_clean3</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  plink --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  plink --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> R</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> hardy = read.table("plink.hwe", header = T) </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> names(hardy)</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> hwe_prob = hardy[which(hardy$P < 0.0000009),] </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> hwe_prob</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> q()</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> plink --file GWAS_clean3 --exclude HWE_out.txt --recode --out GWAS_clean4</ins></div></td></tr>
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Serveradmin
http://statgen.us/index.php?title=Genome-wide_Association-Quality_Control_Exercise&diff=747&oldid=prev
Serveradmin at 17:14, 24 January 2019
2019-01-24T17:14:08Z
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 17:14, 24 January 2019</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l24" >Line 24:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  myvars = c("FID1", "IID1", "FID2", "IID2", "PI_HAT")  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  myvars = c("FID1", "IID1", "FID2", "IID2", "PI_HAT")  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  problem_pairs[myvars]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>  problem_pairs[myvars]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> plink --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> q()</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> plink --file GWAS_clean2 --remove IBS_excluded.txt --recode --out GWAS_clean3</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> plink --file GWAS_clean3 --pheno pheno.txt --pheno-name Aff --hardy</ins></div></td></tr>
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Serveradmin
http://statgen.us/index.php?title=Genome-wide_Association-Quality_Control_Exercise&diff=746&oldid=prev
Serveradmin: Created page with "__NOTITLE__ ==Genome-wide Association-Quality Control Exercise== plink --file GWAS plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind plink --file GWAS_clean_mi..."
2019-01-24T17:04:04Z
<p>Created page with "__NOTITLE__ ==Genome-wide Association-Quality Control Exercise== plink --file GWAS plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind plink --file GWAS_clean_mi..."</p>
<p><b>New page</b></p><div>__NOTITLE__<br />
<br />
==Genome-wide Association-Quality Control Exercise==<br />
<br />
plink --file GWAS<br />
plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind<br />
plink --file GWAS_clean_mind --maf 0.05 --recode --out MAF_greater_5<br />
plink --file GWAS_clean_mind --exclude MAF_greater_5.map --recode --out MAF_less_5<br />
plink --file MAF_greater_5 --geno 0.05 --recode --out MAF_greater_5_clean<br />
plink --file MAF_less_5 --geno 0.01 --recode --out MAF_less_5_clean<br />
plink --file MAF_greater_5_clean --merge MAF_less_5_clean.ped MAF_less_5_clean.map --recode --out GWAS_MAF_clean<br />
plink --file GWAS_MAF_clean --mind 0.03 --recode --out GWAS_clean2<br />
plink --file GWAS_clean2 --check-sex --out GWAS_sex_checking<br />
R<br />
sexcheck = read.table("GWAS_sex_checking.sexcheck", header=T) names(sexcheck)<br />
sex_problem = sexcheck[which(sexcheck$STATUS=="PROBLEM"),] sex_problem<br />
q()<br />
plink --file GWAS_clean2 --genome --out duplicates<br />
R<br />
dups = read.table("duplicates.genome", header = T)<br />
problem_pairs = dups[which(dups$PI_HAT > 0.4),] <br />
problem_pairs<br />
problem_pairs = dups[which(dups$PI_HAT > 0.05),] <br />
myvars = c("FID1", "IID1", "FID2", "IID2", "PI_HAT") <br />
problem_pairs[myvars]</div>
Serveradmin