plink 软件中 cases 和 controls

 

表型2是case。

表型1是control。

 

001、

root@DESKTOP-1N42TVH:/home/test4# ls
outcome.map  outcome.ped
root@DESKTOP-1N42TVH:/home/test4# cat outcome.map
1       s64199.1        0       55910
1       OAR19_64675012.1        0       85204
1       OAR19_64715327.1        0       122948
root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped
DOR     1       0       0       0       1       0 0     C C     G G
DOR     2       0       0       0       1       G G     G C     G G
DOR     3       0       0       0       2       G G     0 0     G G
DOR     4       0       0       0       -9      G G     C C     G G
DOR     5       0       0       0       -9      G G     C C     G G
DOR     6       0       0       0       -9      G G     C C     0 0
root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --recode tab --out test
PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to test.log.
Options in effect:
  --file outcome
  --out test
  --recode tab

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (3 variants, 6 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
3 variants loaded from .bim file.
6 people (0 males, 0 females, 6 ambiguous) loaded from .fam.
Ambiguous sex IDs written to test.nosex .
3 phenotype values loaded from .fam.
Warning: Ignoring phenotypes of missing-sex samples.  If you don't want those
phenotypes to be ignored, use the --allow-no-sex flag.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 6 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.833333.
3 variants and 6 people pass filters and QC.
Among remaining phenotypes, 1 is a case and 2 are controls.  (3 phenotypes are
missing.)
--recode ped to test.ped + test.map ... done.

 

002、

root@DESKTOP-1N42TVH:/home/test4# ls
outcome.map  outcome.ped
root@DESKTOP-1N42TVH:/home/test4# cat outcome.map
1       s64199.1        0       55910
1       OAR19_64675012.1        0       85204
1       OAR19_64715327.1        0       122948
root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped
DOR     1       0       0       0       1       0 0     C C     G G
DOR     2       0       0       0       2       G G     G C     G G
DOR     3       0       0       0       2       G G     0 0     G G
DOR     4       0       0       0       2       G G     C C     G G
DOR     5       0       0       0       2       G G     C C     G G
DOR     6       0       0       0       -9      G G     C C     0 0
root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --recode tab --out test
PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to test.log.
Options in effect:
  --file outcome
  --out test
  --recode tab

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (3 variants, 6 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
3 variants loaded from .bim file.
6 people (0 males, 0 females, 6 ambiguous) loaded from .fam.
Ambiguous sex IDs written to test.nosex .
5 phenotype values loaded from .fam.
Warning: Ignoring phenotypes of missing-sex samples.  If you don't want those
phenotypes to be ignored, use the --allow-no-sex flag.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 6 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.833333.
3 variants and 6 people pass filters and QC.
Among remaining phenotypes, 4 are cases and 1 is a control.  (1 phenotype is
missing.)
--recode ped to test.ped + test.map ... done.

 

003、

root@DESKTOP-1N42TVH:/home/test4# ls
outcome.map  outcome.ped
root@DESKTOP-1N42TVH:/home/test4# cat outcome.map
1       s64199.1        0       55910
1       OAR19_64675012.1        0       85204
1       OAR19_64715327.1        0       122948
root@DESKTOP-1N42TVH:/home/test4# cat outcome.ped
DOR     1       0       0       0       2       0 0     C C     G G
DOR     2       0       0       0       1       G G     G C     G G
DOR     3       0       0       0       1       G G     0 0     G G
DOR     4       0       0       0       1       G G     C C     G G
DOR     5       0       0       0       1       G G     C C     G G
DOR     6       0       0       0       1       G G     C C     0 0
root@DESKTOP-1N42TVH:/home/test4# plink --file outcome --recode tab --out test
PLINK v1.90b6.26 64-bit (2 Apr 2022)           www.cog-genomics.org/plink/1.9/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to test.log.
Options in effect:
  --file outcome
  --out test
  --recode tab

16007 MB RAM detected; reserving 8003 MB for main workspace.
.ped scan complete (for binary autoconversion).
Performing single-pass .bed write (3 variants, 6 people).
--file: test-temporary.bed + test-temporary.bim + test-temporary.fam written.
3 variants loaded from .bim file.
6 people (0 males, 0 females, 6 ambiguous) loaded from .fam.
Ambiguous sex IDs written to test.nosex .
6 phenotype values loaded from .fam.
Warning: Ignoring phenotypes of missing-sex samples.  If you don't want those
phenotypes to be ignored, use the --allow-no-sex flag.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 6 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.833333.
3 variants and 6 people pass filters and QC.
Among remaining phenotypes, 1 is a case and 5 are controls.
--recode ped to test.ped + test.map ... done.