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AJResearchGroup / nsphs_ml_qt

R package for nsphs_ml_qt
GNU General Public License v3.0
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Do PLINK analysis on subset data of #5 #27

Closed richelbilderbeek closed 2 years ago

richelbilderbeek commented 2 years ago 
[richel@sens2021565-bianca ~]$ singularity run nsphs_ml_qt/nsphs_ml_qt.sif /opt/plinkr/plink_1_9_unix/plink --bfile data_issue_5/data_issue_5 --pheno data_issue_5/data_issue_5.phe --allow-no-sex --assoc --out result
'nsphs_ml_qt.sif' running with arguments '/opt/plinkr/plink_1_9_unix/plink --bfile data_issue_5/data_issue_5 --pheno data_issue_5/data_issue_5.phe --allow-no-sex --assoc --out result'
PLINK v1.90b6.22 64-bit (16 Apr 2021)          www.cog-genomics.org/plink/1.9/
(C) 2005-2021 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to result.log.
Options in effect:
  --allow-no-sex
  --assoc
  --bfile data_issue_5/data_issue_5
  --out result
  --pheno data_issue_5/data_issue_5.phe

7317 MB RAM detected; reserving 3658 MB for main workspace.
10 variants loaded from .bim file.
870 people (0 males, 0 females, 870 ambiguous) loaded from .fam.
Ambiguous sex IDs written to result.nosex .
870 phenotype values present after --pheno.
Using 1 thread.
Before main variant filters, 870 founders and 0 nonfounders present.
Calculating allele frequencies... done.
10 variants and 870 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to result.qassoc ... done.
[richel@sens2021565-bianca ~]$ ls
21_create_issue_5_params.log  29_zip_issue_5.log  data_issue_5     nsphs_ml_qt  README.md     result.qassoc
22_create_issue_5_data.log    98_clean_bianca.sh  data_issue_5_ae  plink.log    result.log    richel-sens2021565
25_run_issue_5.log            bin                 GenoCAE          plink.nosex  result.nosex
[richel@sens2021565-bianca ~]$ cat result.qassoc 
 CHR           SNP         BP    NMISS       BETA         SE         R2        T            P 
   1   rs183074751  154452560      870     0.5162      0.149    0.01363    3.463    0.0005594 
   1     rs7526131  154452659      870    -0.9611    0.03401     0.4792   -28.26   4.216e-125 
   1             .  154452779      870     0.2791     0.5037  0.0003536   0.5541       0.5797 
   1             .  154452860      870    -0.7479     0.4501    0.00317   -1.662      0.09697 
   1             .  154452861      870    -0.7479     0.4501    0.00317   -1.662      0.09697 
   1    rs12126142  154452980      870      1.239    0.02812      0.691    44.06   1.466e-223 
   1             .  154453110      870    -0.1942      1.006  4.296e-05  -0.1931       0.8469 
   1             .  154453121      870    -0.1942      1.006  4.296e-05  -0.1931       0.8469 
   1             .  154453122      870    -0.1942      1.006  4.296e-05  -0.1931       0.8469 
   1             .  154453390      870    -0.4463     0.7115  0.0004532  -0.6273       0.5306
richelbilderbeek commented 2 years ago

Note that although a window of 1kb was used, only 10 variants were there.

But, a good find nonetheless!