paturley
commented
3 years ago Hello,
You are right that having the p-value and the z-stat is redundant, but the software uses it as a robustness check to make sure it is reading in the correct columns. If you sumstats done have a p-value column, I suggest you create a new file with the p-values that you calculate yourself.
Best, Patrick
On Fri, Oct 23, 2020 at 1:58 AM Shicheng Guo notifications@github.com wrote:
An interesting error comes out. I have set mtag to use 'Z', I don't know why it still trying to look for 'P'
mtag.py --sumstats bip.sumstats,scz.sumstats --snp_name SNP --z_name Z --n_name N bip.sumstats.txt https://github.com/JonJala/mtag/files/5427572/bip.sumstats.txt scz.sumstats.txt https://github.com/JonJala/mtag/files/5427573/scz.sumstats.txt
2020/10/22/10:51:25 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> <> <> MTAG: Multi-trait Analysis of GWAS <> Version: 1.0.8 <> (C) 2017 Omeed Maghzian, Raymond Walters, and Patrick Turley <> Harvard University Department of Economics / Broad Institute of MIT and Harvard <> GNU General Public License v3 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> <> Note: It is recommended to run your own QC on the input before using this program. <> Software-related correspondence: maghzian@nber.org <> All other correspondence: paturley@broadinstitute.org <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
Calling ./mtag.py \ --z-name Z \ --n-name N \ --snp-name SNP \ --sumstats bip.sumstats.txt,scz.sumstats.txt
2020/10/22/10:51:25 PM Beginning MTAG analysis... 2020/10/22/10:51:25 PM MTAG will use the Z column for analyses. 2020/10/22/10:51:25 PM Read in Trait 1 summary statistics (1000 SNPs) from bip.sumstats ... 2020/10/22/10:51:25 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2020/10/22/10:51:25 PM Munging Trait 1 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><>< 2020/10/22/10:51:25 PM <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> 2020/10/22/10:51:25 PM ERROR converting summary statistics:
2020/10/22/10:51:25 PM Traceback (most recent call last): File "/projects/ps-janssen4/dsci-csb/user/sguo2/bin/mtag/mtag_munge.py", line 801, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find P column.
2020/10/22/10:51:25 PM Conversion finished at Thu Oct 22 22:51:25 2020 2020/10/22/10:51:25 PM Total time elapsed: 0.0s 2020/10/22/10:51:25 PM Could not find P column. Traceback (most recent call last): File "/home/sguo2/janssen4/bin/mtag/mtag.py", line 1567, in
mtag(args) File "/home/sguo2/janssen4/bin/mtag/mtag.py", line 1336, in mtag DATA_U, DATA, args = load_and_merge_data(args) File "/home/sguo2/janssen4/bin/mtag/mtag.py", line 269, in load_and_merge_data GWAS_d[p], sumstats_format[p] = _perform_munge(args, GWAS_d[p], gwas_dat_gen, p) File "/home/sguo2/janssen4/bin/mtag/mtag.py", line 162, in _perform_munge munged_results = munge_sumstats.munge_sumstats(argnames, write_out=False, new_log=False) File "/projects/ps-janssen4/dsci-csb/user/sguo2/bin/mtag/mtag_munge.py", line 801, in munge_sumstats raise ValueError('Could not find {C} column.'.format(C=c)) ValueError: Could not find P column. 2020/10/22/10:51:25 PM Analysis terminated from error at Thu Oct 22 22:51:25 2020 2020/10/22/10:51:25 PM Total time elapsed: 0.01s — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/JonJala/mtag/issues/116, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFBUB5KUG76VSPXI5YWN5W3SMELSBANCNFSM4S4DRNZA .
An interesting error comes out. I have set mtag to use 'Z', I don't know why it still trying to look for 'P'
mtag.py --sumstats bip.sumstats.txt,scz.sumstats.txt --snp_name SNP --z_name Z --n_name Nbip.sumstats.txt scz.sumstats.txt