abdel
New Member
Posts: 8 
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Post by abdel on May 6, 2015 11:34:11 GMT
Is it possible to run a MLMA analysis using multiple GRMs? I tried the --mgrm-gz option as well as just giving multiple GRMs with --grm-gz, but unfortunately both don't seem to work...
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Post by Zhihong Zhu on May 10, 2015 3:36:08 GMT
Hi there,
Can you please transform the GRMs from .gz file to binary file? I usually use "--mgrm" and it works.
CHeers,
Zhihong
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abdel
New Member
Posts: 8
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Post by abdel on May 10, 2015 14:22:32 GMT
Thank you very much!
I tried unzipping it, but unfortunately it still doesn't work..
I use the following command:
gcta64 --mgrm multi_grm --bfile binary_plink_file --pheno phentype_file.pheno --qcovar covariate_file.covs --mlma --out MLMA.multiple_GRMs --thread-num 8
Unfortunately this gives me the following error message:
Error: can not open the file [multi_grm.grm.id] to read.
Which means that GCTA expects 1 GRM with the filename multi_grm instead of multi_grm being the name of a text file containing the filenames of the multiple GRMs.
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Post by Zhihong Zhu on May 11, 2015 23:15:22 GMT
Hi there,
Can you please try the following steps?
1. transform GRM from .gz to .bin file, one GRM by one GRM, eg. gcta64 --grm-gz grmfile --make-grm --out grmbin. (--grm-gz option needs GRM in .gz format)
2. create a txt file (multi_grm.txt) which contain the prefix of those GRM files,
e.g.
/Users/uqzzhu1/Documents/grm1
/Users/uqzzhu1/Documents/grm2
/Users/uqzzhu1/Documents/grm3
3. run the MLMA analysis, e.g. gcta64 --mgrm multi_grm.txt --bfile binary_plink_file --pheno phentype_file.pheno --qcovar covariate_file.covs --mlma --out MLMA.multiple_GRMs --thread-num 8.
Cheers,
Zhihong
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abdel
New Member
Posts: 8
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Post by abdel on May 12, 2015 17:24:08 GMT
Dear Zhihong,
Many thanks for your quick reply!
I have converted the grm's to bin format using --make-grm-bin , and I have also tried converting it to a regular grm with --make-grm. Both options unfortunately do not work.
If I try:
gcta64 --mgrm-bin multi_grm_binary_format --bfile binary_plink_file --pheno phentype_file.pheno --qcovar covariate_file.covs --mlma --out MLMA.multiple_GRMs --thread-num 8
I get the error:
Error: can not open the file [multi_grm_binary_format.grm.id] to read.
Also if I use your command on the binary format as well as on the regular grm-format (so --mgrm instead of --mgrm-bin) it doesn't work (I get the error message above every time).
So I have now tried all three formats (gz, bin, and the regular format), and in all three instances it seems expects the filename of the text-file that contains the prefix of the GRMs (which have very different names) to be the prefix of the GRM file.
I'm using version 1.24.4.
Many thanks again for your time!
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Post by Zhihong Zhu on May 12, 2015 23:31:39 GMT
Hi there,
1. If "multi_grm_binary_format" is not the full name, e.g. prefix name of "multi_grm_binary_format.txt", can you please try "gcta64 --mgrm multi_grm_binary_format.txt ..." ?
2. And It might be because multiple GRMs are not expected in MLMA module. If so, can you please try merging the multiple GRMs into one before run the MLMA?
e.g.
gcta64 --mgrm multi_grm.txt --make-grm --out grm_test
gcta64 --grm grm_test --bfile binary_plink_file --pheno phentype_file.pheno --qcovar covariate_file.covs --mlma --out MLMA.multiple_GRMs --thread-num 8
Cheers,
Zhihong
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Post by Jian Yang on May 29, 2015 1:17:36 GMT
Dear Zhihong, Many thanks for your quick reply! I have converted the grm's to bin format using --make-grm-bin , and I have also tried converting it to a regular grm with --make-grm. Both options unfortunately do not work. If I try: gcta64 --mgrm-bin multi_grm_binary_format --bfile binary_plink_file --pheno phentype_file.pheno --qcovar covariate_file.covs --mlma --out MLMA.multiple_GRMs --thread-num 8 I get the error: Error: can not open the file [multi_grm_binary_format.grm.id] to read. Also if I use your command on the binary format as well as on the regular grm-format (so --mgrm instead of --mgrm-bin) it doesn't work (I get the error message above every time). So I have now tried all three formats (gz, bin, and the regular format), and in all three instances it seems expects the filename of the text-file that contains the prefix of the GRMs (which have very different names) to be the prefix of the GRM file. I'm using version 1.24.4. Many thanks again for your time! MLMA with multiple GRMs will be available in next GCTA release. |
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abdel
New Member
Posts: 8
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Post by abdel on May 29, 2015 13:12:50 GMT
Thank you very much Jian! Looking forward to the next release  |
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Post by Jian Yang on Jun 10, 2015 6:15:47 GMT
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abdel
New Member
Posts: 8
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Post by abdel on Jun 10, 2015 19:58:34 GMT
Thanks! Big fan of the other options you added |
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