association tests

[Cristhiam de Jesus Hernandez Martinez]

Hi all

I am trying to make a linear association (case-control) in plink2

with the following command:

plink2 --pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr --pheno FID_IID_2Affected_or_1Unaffected.pheno --glm

I tested some other commands :

plink2 --pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr --pheno FID_IID_2Affected_or_1Unaffected.pheno --glm [2Affected_or_1Unaffected]

 

plink2 --pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr --pheno FID_IID_2Affected_or_1Unaffected.pheno --glm \--covar tmp.cov \--parameters 2Affected_or_1Unaffected

 

plink2 --pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr --pheno FID_IID_2Affected_or_1Unaffected.pheno --glm--covar3

and the answer I always got for the different commands tested was erro:

 Error: Unrecognized flag ˂--glm--parameters>

Any suggestions as to what might be the problem? or the recommended command to compare control group with test group. The data I am analyzing is methylation array.

 

Thanks

[Christopher Chang]

You need to post the exact .log file from one of your failed runs, because this error is probably caused by something you're doing with backslashes and spaces that you did not fully reproduce in your post.

[Cristhiam de Jesus Hernandez Martinez]

Dear Chrch,

I have 24 samples (cases vs control) and I am trying to make a link in plink 2 with the following command:

plink2\

 --pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr\

 --pheno C6_vs_G6.pheno\

 --glm\

 --allow-no-covar

when I execute the command it says flag --allow-no-covar is not recognizable

what am i doing wrong, how can i reverse this? i am new to plink and learning.

[Christopher Chang]

The correct syntax is "--glm allow-no-covars", not "--glm --allow-no-covar".  There is no --allow-no-covar flag in the index; there is an 'allow-no-covars' modifier listed in the --glm documentation.

[Cristhiam de Jesus Hernandez Martinez]

Dear Chrch
I am trying to make an extraction of data that is significant 0.05, when I execute the following command 

plink2\

 --pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr_sort-vars\

 --pheno CC_vs_GC.pheno\

 --geno 0.084\

--out plink2.geno0.084\

--extract Significant0.05CC_vr_GC.txt\

 --export oxford[-v2]

it gives error -- export requires at least one output format.
what would be your suggestion
thanks

[Matthew Maher]

you gave a format of "oxford[-v2]" which is not valid. 

You no doubt meant either:

oxford

or

oxford-v2

oxford[-v2] is just syntax-lingo meaning "the -v2 suffix is optional"

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[Cristhiam de Jesus Hernandez Martinez]

Thank you very much, I am trying to get the P value of the comparisons of the control group with the test group, I initially ran the following command

plink2\

--pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr\

--make-pgen\

--sort-vars\

--out SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr_sort-vars

then I made the filtering of the P values less than or equal to 0.05 with the following command

plink2\

--pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr_sort-vars\

--pheno C6_vs_G6.pheno\

--glm allow-no-covars\

--geno 0.084\

--out plink2.geno0.084\

--pfilter 0.05

from that file copy the column 3 "ID" with the significant IDs of the cg probe and paste them in a text file plink2.geno0.084.Affected.glm.logistic.hybrid_cgProbeIDsSignificant

After doing this I ran the following command, and this is where the problem is that so far I could not solve it and need some guidance

plink2 \

--pfile SesameBetas.csv_winfinium-mouse-methylation-manifest-file-csv_IlmnID_CHR_MAPINFO_Build_mm10_FID_IID2_NoNAChr_sort-vars\

--pheno C6_vs_G6.pheno\

--geno 0.084\

--out plink2.geno0.084\

--extract plink2.geno0.084.Affected.glm.logistic.hybrid_cgProbeIDsSignificant\

--export A-transpose

attached you can find the text file with the file ID Significant0.05C6_vr_G6.txt
please help me