The munging of 2 summary statistics started at 2025-03-05 09:28:40.332976
Reading in reference file
Reading summary statistics for SCZ_chr1.txt BIP_chr1.txt. Please note that this step usually takes a few minutes due to the size of summary statistic files.
All files loaded into R!



Munging file: SCZ_chr1.txt
Found an NEFF column for sample size. 

Please note that this is likely effective sample size and should only be used for liability h^2 conversion for binary traits and that it should reflect the sum of effective sample sizes across cohorts.

Be aware that some NEFF columns reflect half of the effective sample size; the function will automatically double the column names if recognized [check above in .log file to determine if this is the case].
If the Neff value is halved in the summary stats, but not recognized by the munge function, this should be manually doubled prior to running munge.
Interpreting the ID column as the SNP column.
Interpreting the A1 column as the A1 column.
Interpreting the A2 column as the A2 column.
Interpreting the BETA column as the effect column.
Interpreting the IMPINFO column as the INFO column.
Interpreting the PVAL column as the P column.
Interpreting the NEFF column as the N column.
Interpreting the SE column as the SE column.
Merging file:SCZ_chr1.txt with the reference file:eur_w_ld_chr/w_hm3.snplist
588630 rows present in the full SCZ_chr1.txt summary statistics file.
491146 rows were removed from the SCZ_chr1.txt summary statistics file as the rs-ids for these rows were not present in the reference file.
3923 rows were removed from the SCZ_chr1.txt summary statistics file due to INFO values below the designated threshold of0.9
No MAF column, cannot filter on MAF, which may influence results
93561SNPs are left in the summary statistics file SCZ_chr1.txt after QC.
I am done munging file: SCZ_chr1.txt
The file is saved as SCZ.sumstats.gz in the current working directory.



Munging file: BIP_chr1.txt
Found an NEFFDIV2 column for sample size. 

Please note that this is likely effective sample size cut in half. The function is automatically doubling this value. This should only be used for liability h^2 conversion for binary traits and that it should reflect the sum of effective sample sizes across cohorts.
Found an NEFF column for sample size. 

Please note that this is likely effective sample size and should only be used for liability h^2 conversion for binary traits and that it should reflect the sum of effective sample sizes across cohorts.

Be aware that some NEFF columns reflect half of the effective sample size; the function will automatically double the column names if recognized [check above in .log file to determine if this is the case].
If the Neff value is halved in the summary stats, but not recognized by the munge function, this should be manually doubled prior to running munge.
Interpreting the ID column as the SNP column.
Interpreting the A1 column as the A1 column.
Interpreting the A2 column as the A2 column.
Interpreting the BETA column as the effect column.
Interpreting the IMPINFO column as the INFO column.
Interpreting the PVAL column as the P column.
Interpreting the NEFF column as the N column.
Interpreting the SE column as the SE column.
Interpreting the DIRE column as the DIRECTION column.
Merging file:BIP_chr1.txt with the reference file:eur_w_ld_chr/w_hm3.snplist
584331 rows present in the full BIP_chr1.txt summary statistics file.
486978 rows were removed from the BIP_chr1.txt summary statistics file as the rs-ids for these rows were not present in the reference file.
4595 rows were removed from the BIP_chr1.txt summary statistics file due to INFO values below the designated threshold of0.9
No MAF column, cannot filter on MAF, which may influence results
92758SNPs are left in the summary statistics file BIP_chr1.txt after QC.
I am done munging file: BIP_chr1.txt
The file is saved as BIP.sumstats.gz in the current working directory.
     
Munging was completed at 2025-03-05 09:28:53.500415
The munging of all files took 0 minutes and 13.1674394607544 seconds
Please check the .log file(s) to ensure that all columns were interpreted correctly and no warnings were issued for any of the summary statistics files