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Different columns in the result table #6

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shenweima opened this issue Oct 18, 2021 · 3 comments
Open

Different columns in the result table #6

shenweima opened this issue Oct 18, 2021 · 3 comments

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@shenweima
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Columns order in the manual
image
Columns order my result
image

which is right?
@gc5k
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gc5k commented Oct 18, 2021

columns in the screen snap is correct.
I've updated the wiki.
thanks.

@shenweima
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In my result, the p value is normal, but all the PGC value are > 0.0001.
image

log information

****************************************************************
 GEAR [GEnetic Analysis Repository]
 (C) 2013 Guo-Bo Chen, Zhi-Xiang Zhu
 Branch master
 Commit 16a202fa7b6ed52d10ca34afe0647e2b11dab7f4
 Built on Sat Apr 06 22:51:21 CST 2019
****************************************************************

[INFO] Subcommand: eigengwas
[INFO] Options in effect: 
[INFO] 	--bfile ../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed
[INFO] 	--ev 2
[INFO] 	--keep CC_LA_sample.list
[INFO] 	--maf 0.05
[INFO] 	--out eigen_CCvsLA
[INFO] 
[INFO] Analysis started: Sun Oct 17 15:50:38 CST 2021
[INFO] 
[INFO] Reading '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bim'.
[INFO] Read 52186945 marker(s) from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bim'
[INFO] Selected marker(s): 52186945
[INFO] 52186945 SNPs were remained for analysis.
[INFO] Read 638 individuals from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.fam'.
[INFO] Reading '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bed'.
[INFO] Reading data in PLINK SNP-major mode.
[INFO] It took 12 minutes 39 seconds to read the bed data.
[INFO] Individual number: 638
[INFO] Read 279 individuals from the keep-individual file 'CC_LA_sample.list'.
[INFO] 279 individuals were matched for analysis.
[INFO] 
[INFO] Calculating locus statistics with 1 threads.
[INFO] Average MAF: 0.2375
[INFO] Average variance: 0.3215
[INFO] Average missing rate: 0.0000
[INFO] 
[INFO] Quality control for SNPs...
[INFO] 3006374 SNPs were excluded because did not pass maf threshold 0.05.
[INFO] 49180571 SNPs were remained for analysis.
[INFO] 
[INFO] Making additive genetic relatedness matrix...
[INFO] Standardizing genotypes (additive)...
[INFO] Calculating GA with 1 thread.
[INFO] 
[INFO] Writing GRM scores into 'eigen_CCvsLA.grm.gz'.
[INFO] Writing 279 individuals' information into 'eigen_CCvsLA.grm.id'.
[INFO] Mean of genetic relatedness is: -0.0950
[INFO] Sampling variance of genetic relatedness is: 0.6602
[INFO] Effective sample size is: 11.5250
[INFO] Effective number of genome segments is: 1.5147
[INFO] It took 1 hour 6 minutes 52 seconds to make additive genetic relatedness matrix.
[INFO] 
---------Generating eigenvectors---------
[INFO] Read 279 samples from 'eigen_CCvsLA.grm.id'.
[INFO] Read 279 samples from 'CC_LA_sample.list'.
[INFO] 279 samples were matched across 2 files.
[INFO] 
[INFO] The #1 eigenvalue is 178.09581839597385.
[INFO] The #2 eigenvalue is 102.66683381230396.
[INFO] Saved the eigenvalues in 'eigen_CCvsLA.eigenval'.
[INFO] Saved the top 2 eigenvectors in 'eigen_CCvsLA.eigenvec'.
[INFO] Saved the correlation matrix in 'eigen_CCvsLA.crm'.
[INFO] 
---------Running EigenGWAS (Additive model) for the 1th eigenvector.
[INFO] Reading '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bim'.
[INFO] Read 52186945 marker(s) from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bim'
[INFO] Selected marker(s): 52186945
[INFO] 52186945 SNPs were remained for analysis.
[INFO] Read 638 individuals from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.fam'.
[INFO] Reading '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bed'.
[INFO] Reading data in PLINK SNP-major mode.
[INFO] It took 14 minutes 9 seconds to read the bed data.
[INFO] Individual number: 638
[INFO] Read 638 samples from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.fam'.
[INFO] Read 279 samples from 'eigen_CCvsLA.eigenvec'.
[INFO] Read 279 samples from 'CC_LA_sample.list'.
[INFO] 279 samples were matched across 3 files.
[INFO] 
[INFO] 279 individuals were matched for analysis.
[INFO] 
[INFO] Calculating locus statistics with 1 threads.
[INFO] Average MAF: 0.2375
[INFO] Average variance: 0.3215
[INFO] Average missing rate: 0.0000
[INFO] 
[INFO] Quality control for SNPs...
[INFO] 3006374 SNPs were excluded because did not pass maf threshold 0.05.
[INFO] 49180571 SNPs were remained for analysis.
[INFO] Calculating eGWAS with 1 thread.
[INFO] Median of p values is 1.3510898375646008E-6
[INFO] Lambda GC is: 51.32791304714518
[INFO] Saved EigenGWAS results in 'eigen_CCvsLA.1.egwas'.
[INFO] 
---------Running EigenGWAS (Additive model) for the 2th eigenvector.
[INFO] Reading '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bim'.
[INFO] Read 52186945 marker(s) from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bim'
[INFO] Selected marker(s): 52186945
[INFO] 52186945 SNPs were remained for analysis.
[INFO] Read 638 individuals from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.fam'.
[INFO] Reading '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.bed'.
[INFO] Reading data in PLINK SNP-major mode.
[INFO] It took 13 minutes 37 seconds to read the bed data.
[INFO] Individual number: 638
[INFO] Read 638 samples from '../snp_and_indel/all638.snp.indel.edit.het.reheader.maf0.05.missingrate0.25.imputed.fam'.
[INFO] Read 279 samples from 'eigen_CCvsLA.eigenvec'.
[INFO] Read 279 samples from 'CC_LA_sample.list'.
[INFO] 279 samples were matched across 3 files.
[INFO] 
[INFO] 279 individuals were matched for analysis.
[INFO] 
[INFO] Calculating locus statistics with 1 threads.
[INFO] Average MAF: 0.2375
[INFO] Average variance: 0.3215
[INFO] Average missing rate: 0.0000
[INFO] 
[INFO] Quality control for SNPs...
[INFO] 3006374 SNPs were excluded because did not pass maf threshold 0.05.
[INFO] 49180571 SNPs were remained for analysis.
[INFO] Calculating eGWAS with 1 thread.
[INFO] Median of p values is 0.010273208208183338
[INFO] Lambda GC is: 14.479879106900347
[INFO] Saved EigenGWAS results in 'eigen_CCvsLA.2.egwas'.
[INFO] 
[INFO] Analysis finished: Sun Oct 17 19:08:13 CST 2021
[INFO] Peak memory consumption: 88.9 GB
[INFO] It took 3 hours 17 minutes 34 seconds to run the command.

@gc5k
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gc5k commented Oct 20, 2021

"
[INFO] The #1 eigenvalue is 178.09581839597385.
[INFO] The #2 eigenvalue is 102.66683381230396.
"

"
[INFO] Lambda GC is: 51.32791304714518
"
"
[INFO] Lambda GC is: 14.479879106900347
"

We have noticed the problem for many for a while, and you are not alone. From eigenvalue and GC, it seems that the population structure is too strong, or the sample is not a random sample but from a highly selected elite lines.

When the eigenvalue is large, EigenGWAS is too conservative. You can safely pick up the signal peaks and put forward for your analysis.
We have been testing evaluate solutions possible. However, we don't have crystal statement for how to adjust it in straight.

From my experience, your data quality is good. Pretty good actually!

Will have you posted for possible update.

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@gc5k @shenweima