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Update README.md
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jxzb1988 authored Oct 7, 2021
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Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions README.md
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Expand Up @@ -72,7 +72,7 @@ Given that we have 5 tissues/conditions, named as condition1, condition2, condit

For phenotype, the phenotype files ((g+1)x(n+1) matrix, g is the number of explored genes, and n is the sample size. Both column and row names should be included) are named as phenotype_file_1, phenotype_file2, phenotype_file3, phentoype_file4, phenotype_file5;

For genotype, the binary plink-format genotype files are named as genotype_file_1, genotype_file_2, genotype_file_3, genotype_file_4, genotype_file_5;
For genotype, the binary plink-format genotype files are named as genotype_file_1, genotype_file_2, genotype_file_3, genotype_file_4, genotype_file_5; To speed up mmQTL running, split genotype into chromosomes.

You need an annotation file for the exploed features in bed format: chr start end feature_name;

Expand All @@ -95,16 +95,16 @@ path/to/phentoype_file_4
path/to/phentoype_file_5
```

-Z: specify the location of the file containing the location of genotype files for each tissue/condition. The format for the genotype should be in PLINK format. To speed up mmQTL running, split genotype into chromosomes.
-Z: specify the location of the file containing the location of genotype files for each tissue/condition. The format for the genotype should be in PLINK format.

This file should be:

```
path/to/genotype_file_1
path/to/genotype_file_2
path/to/enotype_file_3
path/to/enotype_file_4
path/to/enotype_file_5
path/to/genotype_file_3
path/to/genotype_file_4
path/to/genotype_file_5
```


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