sync with updates

CMakeLists.txt

@@ -15,4 +15,5 @@ IF (NOT DEFINED DEBUG)
 ENDIF()
 ADD_DEFINITIONS(-DDEBUG=${DEBUG})
 
-add_executable(RHEmc src/rhemc_ldsc_her_def_stream.cpp src/genotype.cpp src/storage.cpp)
+add_executable(RHEmc src/rhemc_cov_ldsc_her_def.cpp src/genotype.cpp src/storage.cpp)
+add_executable(RHEmc_dom src/dom_jack_stream.cpp src/genotype.cpp src/storage.cpp)

README.md

@@ -6,7 +6,7 @@ Randomized Heritability Estimation for Multi-variance Components
 ## Prerequisites
 The following packages are required on a linux machine to compile and use the software package.
 ```
-g++
+g++ (4.4.7)
 cmake
 make
 ```
@@ -27,17 +27,23 @@ An executable file named RHEmc will be in build folder after the installation st
  ```
  ./RHEmc <command_line arguments>
 ```
+To estimate dominance heritability and additve heritability jointly run :
+
+```
+ ./RHEmc_dom <command_line arguments>
+```
+
 ## Parameters
 
 ```
 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)
+num_vec (-k) : The number of random vectors (10 is recommended). 
+num_block (-jn): The number of jackknife blocks. (100 or 22 are recommended). The higher number of jackknife blocks the higher memory usage.
 out_put (-o): The path of output file.
-memory efficent mode (-mem): The flag states whether to use a memory effecient version of code. The memory efficient version is a little slower  than the not efficient version (default: false)
+
 
 ```
 ## File formats
@@ -47,17 +53,24 @@ Phenotype: It must have a header in the following format: FID IID name_of_phenot
 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 " ")
 
-1) Order of individuals must be same in phenotype, gentype and covariate files.
-2) Order of SNPs must be same in bim file and annotation file.
-3) Annotation file does not have a header.
+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.
+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  :
 ```
-```
-
 
+chmod +x test.sh
+./test.sh
 
+```
 
+## Citation
+```
+Pazokitoroudi, A., Wu, Y., Burch, K.S. et al. Efficient variance components analysis across millions of genomes. Nat Commun 11, 4020 (2020). https://doi.org/10.1038/s41467-020-17576-9
+```