Recent changes to BLUP

BLUP modified by Guobo Chen

Guobo Chen — Tue, 12 Nov 2013 14:57:03 -0000

--- v9
+++ v10
@@ -19,7 +19,7 @@
 --file or --bfile
 Specify the PLINK format data files. See [PLINK document](http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) for details.

---phe
+--pheno
 Specify the phenotype file, i.e. the individual eigenvectors. The phenotype file should consist of at least 3 columns. The fist column is family IDs. The second column is individual IDs. Starting from the third column, each column records the phenotypes of all the individuals of a trait.

 --out
@@ -27,5 +27,5 @@

 **Example**
-gear bluppca --grm-bin test --bfile test --phe test.eigenvec --out test
-gear bluppca --grm test --bfile test --phe test.eigenvec --out test
+gear bluppca --grm-bin test --bfile test --pheno test.eigenvec --out test
+gear bluppca --grm test --bfile test --pheno test.eigenvec --out test

BLUP modified by Zhixiang Zhu

Zhixiang Zhu — Sun, 10 Nov 2013 09:26:33 -0000

--- v8
+++ v9
@@ -27,5 +27,5 @@

 **Example**
-gear bluppca --grm-bin test --bfile test --pheno test.eigenvec --out test
-gear bluppca --grm test --bfile test --pheno test.eigenvec --out test
+gear bluppca --grm-bin test --bfile test --phe test.eigenvec --out test
+gear bluppca --grm test --bfile test --phe test.eigenvec --out test

BLUP modified by Zhixiang Zhu

Zhixiang Zhu — Sun, 10 Nov 2013 09:25:55 -0000

--- v7
+++ v8
@@ -19,7 +19,7 @@
 --file or --bfile
 Specify the PLINK format data files. See [PLINK document](http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) for details.

---pheno
+--phe
 Specify the phenotype file, i.e. the individual eigenvectors. The phenotype file should consist of at least 3 columns. The fist column is family IDs. The second column is individual IDs. Starting from the third column, each column records the phenotypes of all the individuals of a trait.

 --out

BLUP modified by Zhixiang Zhu

Zhixiang Zhu — Sun, 10 Nov 2013 02:54:21 -0000

--- v6
+++ v7
@@ -17,7 +17,7 @@
 Specify the genetic relationship matrix (GRM). The GRM is the A matrix mentioned in the algorithm, which quantifies the genetic relatedness between individuals over M SNPs. See [GCTA document](http://www.complextraitgenomics.com/software/gcta/manipulation_grm.html) for details.

 --file or --bfile
-Specify the PLINK format data files. See [PLINK document](http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) for detailes.
+Specify the PLINK format data files. See [PLINK document](http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) for details.

 --pheno
 Specify the phenotype file, i.e. the individual eigenvectors. The phenotype file should consist of at least 3 columns. The fist column is family IDs. The second column is individual IDs. Starting from the third column, each column records the phenotypes of all the individuals of a trait.

BLUP modified by Zhixiang Zhu

Zhixiang Zhu — Sun, 10 Nov 2013 02:51:50 -0000

--- v5
+++ v6
@@ -11,7 +11,7 @@
 **Subcommand: ** bluppca

-**Available options**
+**Available Options**

 --grm-bin, --grm or --grm-gz
 Specify the genetic relationship matrix (GRM). The GRM is the A matrix mentioned in the algorithm, which quantifies the genetic relatedness between individuals over M SNPs. See [GCTA document](http://www.complextraitgenomics.com/software/gcta/manipulation_grm.html) for details.

BLUP modified by Zhixiang Zhu

Zhixiang Zhu — Sun, 10 Nov 2013 02:51:23 -0000

--- v4
+++ v5
@@ -10,7 +10,8 @@

 **Subcommand: ** bluppca

-Available options
+
+**Available options**

 --grm-bin, --grm or --grm-gz
 Specify the genetic relationship matrix (GRM). The GRM is the A matrix mentioned in the algorithm, which quantifies the genetic relatedness between individuals over M SNPs. See [GCTA document](http://www.complextraitgenomics.com/software/gcta/manipulation_grm.html) for details.

BLUP modified by Zhixiang Zhu

Zhixiang Zhu — Sun, 10 Nov 2013 02:50:47 -0000

--- v3
+++ v4
@@ -1,26 +1,30 @@
 __BLUP PCA__
+* * *
+
 It is a novel method for calculating eigenvector for M SNPs in a sample with N individuals (given M>>N).
 The method is a two-step procedure.

 In step 1, the PCA is implemented on a A (N X N) matrix, and the individual eigenvector over the first K space can be calculated.
 In step 2, the BLUP is used to estimate the effects for M SNPs for each SNP eigenvector.

-  

-Master command
---bluppca
+**Subcommand: ** bluppca

-Other options
---grm-bin or --grm
-The grm matrix is the A matrix, which quantifies the genetic relatedness between individuals over M SNPs.
+Available options

---bfile
-The binary file for the reference sample.
+--grm-bin, --grm or --grm-gz
+Specify the genetic relationship matrix (GRM). The GRM is the A matrix mentioned in the algorithm, which quantifies the genetic relatedness between individuals over M SNPs. See [GCTA document](http://www.complextraitgenomics.com/software/gcta/manipulation_grm.html) for details.
+
+--file or --bfile
+Specify the PLINK format data files. See [PLINK document](http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) for detailes.

 --pheno
-The individual eigenvector.
+Specify the phenotype file, i.e. the individual eigenvectors. The phenotype file should consist of at least 3 columns. The fist column is family IDs. The second column is individual IDs. Starting from the third column, each column records the phenotypes of all the individuals of a trait.

-Example
-gear --bluppca --grm-bin test --bfile test --pheno test.eigenvec --out test
-gear --bluppca --grm test --bfile test --pheno test.eigenvec --out test
+--out
+Specify the output root filename. The result is outputted to a .blup file.

+
+**Example**
+gear bluppca --grm-bin test --bfile test --pheno test.eigenvec --out test
+gear bluppca --grm test --bfile test --pheno test.eigenvec --out test

BLUP modified by Guobo Chen

Guobo Chen — Mon, 04 Nov 2013 11:23:34 -0000

--- v2
+++ v3
@@ -1,21 +1,26 @@
 __BLUP PCA__
-It is a novel method for calculating eigenvector for M snp markers in a sample with N individuals (given M>>N).
-More testing is required.
+It is a novel method for calculating eigenvector for M SNPs in a sample with N individuals (given M>>N).
+The method is a two-step procedure.
+
+In step 1, the PCA is implemented on a A (N X N) matrix, and the individual eigenvector over the first K space can be calculated.
+In step 2, the BLUP is used to estimate the effects for M SNPs for each SNP eigenvector.
+
+

 Master command
 --bluppca

 Other options
---grm-bin
-The grm matrix.
+--grm-bin or --grm
+The grm matrix is the A matrix, which quantifies the genetic relatedness between individuals over M SNPs.

 --bfile
-The binary file.
+The binary file for the reference sample.

 --pheno
-The individual eigenvector
-
+The individual eigenvector.

 Example
 gear --bluppca --grm-bin test --bfile test --pheno test.eigenvec --out test
+gear --bluppca --grm test --bfile test --pheno test.eigenvec --out test

BLUPPCA modified by Guobo Chen

Guobo Chen — Sun, 03 Nov 2013 07:57:09 -0000

bluppca modified by Guobo Chen

Guobo Chen — Tue, 03 Sep 2013 01:56:24 -0000

BLUP PCA
It is a novel method for calculating eigenvector for M snp markers in a sample with N individuals (given M>>N).
More testing is required.

Master command
--bluppca

Other options
--grm-bin
The grm matrix.

--bfile
The binary file.

--pheno
The individual eigenvector

Example
gear --bluppca --grm-bin test --bfile test --pheno test.eigenvec --out test