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Update Input format authored by Apolline GALLOIS's avatar Apolline GALLOIS
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Input-format.md
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...@@ -9,8 +9,8 @@ Example: ...@@ -9,8 +9,8 @@ Example:
1 | rs123456 | 7568 | 15411 | A | T 1 | rs123456 | 7568 | 15411 | A | T
5 | rs6715 | 89863 | 41347 | G | A 5 | rs6715 | 89863 | 41347 | G | A
21 | rs75354 | 148962 | 305716 | C | A 21 | rs75354 | 148962 | 305716 | C | A
### **Genotypes raw file** ### **Genotypes raw file**
This is a PLINK file, with columns separated by spaces and a header line. It contains one line per sample with V+6 fields, where V is the number of variants. This is a PLINK file, with columns separated by spaces and a header line. It contains one line per sample with V+6 fields, where V is the number of variants.
...@@ -26,8 +26,8 @@ FID | IID | PAT | MAT | SEX | PHENOTYPE | SNP1 | SNP2 | SNP3 | .......... ...@@ -26,8 +26,8 @@ FID | IID | PAT | MAT | SEX | PHENOTYPE | SNP1 | SNP2 | SNP3 | ..........
:---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---: | :---:
1 | 1 | 0 | 0 | 2 | 0 | 0 | 1 | 2 | .......... 1 | 1 | 0 | 0 | 2 | 0 | 0 | 1 | 2 | ..........
2 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 2 | .......... 2 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 2 | ..........
### **Phenotypes file** ### **Phenotypes file**
This is a text file, with columns separated by tabulations and a header line. In contains one line per individual. First column must be the individual ID. This is a text file, with columns separated by tabulations and a header line. In contains one line per individual. First column must be the individual ID.
...@@ -39,8 +39,8 @@ ID | Sex | Age | LDL-C | HDL-C | HDL-D | HDL-TG | .......... ...@@ -39,8 +39,8 @@ ID | Sex | Age | LDL-C | HDL-C | HDL-D | HDL-TG | ..........
1 | 1 | 45 | 0.1 | 0.48 | 0.85 | 0.89 | .......... 1 | 1 | 45 | 0.1 | 0.48 | 0.85 | 0.89 | ..........
2 | 1 | 32 | 0.2 | 0.65 | 0.1 | 0.41 | .......... 2 | 1 | 32 | 0.2 | 0.65 | 0.1 | 0.41 | ..........
3 | 2 | 47 | 0.8 | 0.21 | 0.5 | 0.3 | .......... 3 | 2 | 47 | 0.8 | 0.21 | 0.5 | 0.3 | ..........
### **Phenotypes summary file** ### **Phenotypes summary file**
This is a csv file with columns separated by commas and a header line. This file aims at describing the role of each variable contained in the phenotypes file. For each selected variable, the user must provide a label and a binary indicator for classification as confounding factors (i.e. variables systematically included as covariates), outcome (i.e. each single variable that will be treated as a primary outcome) and candidate covariates (i.e. variables that will be assessed by CMS for inclusion as a covariate). This is a csv file with columns separated by commas and a header line. This file aims at describing the role of each variable contained in the phenotypes file. For each selected variable, the user must provide a label and a binary indicator for classification as confounding factors (i.e. variables systematically included as covariates), outcome (i.e. each single variable that will be treated as a primary outcome) and candidate covariates (i.e. variables that will be assessed by CMS for inclusion as a covariate).
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