Update README.md

add description of multiple phenotypes version

README.md

@@ -4,9 +4,9 @@ Randomized Haseman–Elston regression for Multi-variance Components
 
 
 ## Prerequisites
-The following packages are required on a linux machine to compile and use the software package.
+The following packages are required on a Linux machine to compile and use the software package.
 ```
-g++ (4.4.7)
+g++ 
 cmake
 make
 ```
@@ -23,51 +23,61 @@ make
 ```
 
 # Documentation for RHE-mc
-An executable file named RHEmc will be in build folder after the installation steps. Run RHE-mc as follows:
+An executable file named RHEmc will be in the build folder after the installation steps. Run RHE-mc as follows:
  ```
  ./RHEmc <command_line arguments>
 ```
-To run the highly memory efficient version : (-jn 1000 is recommended when there are many overlapping annotations or small annotations)
+To run the high memory efficient version : (-jn 1000 is recommended when there are many overlapping annotations or small annotations)
+
+The memory usage of RHEmc_mem does not depend on the number of jackknife blocks.
 
-The memory usage of RHEmc_mem does not depend on number of jackknife blocks.
 ```
 ./RHEmc_mem <command_line arguments>
 
 ```
-To estimate dominance heritability and additve heritability jointly run :
+To estimate dominance heritability and additive heritability jointly run :
 
 ```
  ./RHEmc_dom <command_line arguments>
 ```
 
+To run the multiple phenotypes version:
+
+```
+./RHEmc_mp <command_line arguments>
+
+```
+
+
+
 ## Parameters
 
 ```
-genotype (-g) : The path of genotype file
+genotype (-g): The path of genotype file
 phenotype (-p): The path of phenotype file
 covariate (-c): The path of covariate file
 annotation (-annot): The path of annotation file.
-num_vec (-k) : The number of random vectors (10 is recommended). 
-num_block (-jn): The number of jackknife blocks. (100 is recommended). The higher number of jackknife blocks the higher memory usage.
-out_put (-o): The path of output file.
+num_vec (-k): The number of random vectors (10 is recommended). 
+num_block (-jn): The number of jackknife blocks. (100 is recommended). The higher number of jackknife blocks the higher the memory usage.
+out_put (-o): The path of the output file.
 
 
 ```
 ## File formats
 ```
-Genotype : It must be in bed format.
-Phenotype: It must have a header in the following format: FID IID name_of_phenotype
+Genotype: It must be in bed format.
+Phenotype: It must have a header in the following format: FID IID name_of_phenotype. In case of multiple phenotypes:  FID IID name_of_phen_1 name_of_phen_2  . . .   name_of_phen_n 
 Covariate: It must have a header in the following format: FID IID name_of_cov_1 name_of_cov_2  . . .   name_of_cov_n
-Annotation: It has M rows (M=number  of SNPs) and K columns (K=number of annotations). If SNP i belongs to annotation j, then there is  "1" in row i and column j. Otherwise there is "0". (delimiter is " ")
+Annotation: It has M rows (M=number  of SNPs) and K columns (K=number of annotations). If SNP i belongs to annotation j, then there is  "1" in row i and column j. Otherwise, there is "0". (delimiter is " ")
 
-1) Number and order of individuals must be same in phenotype, gentype and covariate files.
-2) Number and order of SNPs must be same in bim file and annotation file.
+1) Number and order of individuals must be the same in phenotype, genotype, and covariate files.
+2) Number and order of SNPs must be the same in the bim file and annotation file.
 3) Annotation file does not have a header. The code supports overlapping annotations (e.g : functional annotation)
 4) SNPs with MAF=0 must be excluded from the genotype file.
 5) RHE-mc excludes individuals with NA values in the phenotype file from the analysis.
 ```
 ## Toy example 
-To make sure that everything works well, sample files are provided in example directory. Look at test.sh file and run it  :
+To make sure that everything works well, sample files are provided in the example directory. Look at test.sh file and run it  :
 ```
 
 chmod +x test.sh