Recent changes to propc

propc modified by Guobo Chen

Guobo Chen — Fri, 12 Jun 2015 05:04:37 -0000

--- v8
+++ v9
@@ -81,6 +81,7 @@

 ~~~~
 java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --out pur
+java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score-gz score.txt.gz --out pur
 ~~~~

 Inside batch.txt is

propc modified by Guobo Chen

Guobo Chen — Fri, 05 Jun 2015 06:08:23 -0000

--- v7
+++ v8
@@ -92,7 +92,7 @@
 The illustration of the projected pc for Puerto Ricans as well as HapMap reference is as below
 ![pur](https://sourceforge.net/p/gbchen/wiki/propc/attachment/pur.png).

-The HapMap reference genotype data, the eigenvector scores can be found [here](http://sourceforge.net/projects/gbchen/files/Demo/proBatch.zip/download). The demo is also included.
+The HapMap reference genotype data, the eigenvector scores can be found [***HERE***](http://sourceforge.net/projects/gbchen/files/Demo/proBatch.zip/download). The demo is also included.

 In addtion, the above procedure can also be implemented step by step if the user feels interested.

propc modified by Guobo Chen

Guobo Chen — Thu, 21 May 2015 08:25:01 -0000

--- v6
+++ v7
@@ -78,6 +78,7 @@
 In the examples below, it shows how to generate projected PC for Puerto Rican cohort in [1000 Genome projects](http://www.1000genomes.org/category/frequently-asked-questions/samples)

 **Example 1** generating projected pc using batch solution
+
 ~~~~
 java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --out pur
 ~~~~
@@ -94,6 +95,7 @@
 The HapMap reference genotype data, the eigenvector scores can be found [here](http://sourceforge.net/projects/gbchen/files/Demo/proBatch.zip/download). The demo is also included.

 In addtion, the above procedure can also be implemented step by step if the user feels interested.
+
 ~~~~~~~~~~~~~~~~~
 java -Xmx15G -jar /path/gear.jar comsnp --bfiles PUR HapMap --out score
 java -Xmx15G -jar /path/gear.jar propc --bfile PUR --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target

propc modified by Guobo Chen

Guobo Chen — Sun, 17 May 2015 02:07:47 -0000

--- v5
+++ v6
@@ -77,14 +77,7 @@

 In the examples below, it shows how to generate projected PC for Puerto Rican cohort in [1000 Genome projects](http://www.1000genomes.org/category/frequently-asked-questions/samples)

-**Example 1** generating projected pc for the target sample and the HapMap samples together.
-~~~~~~~~~~~~~~~~~
- java -Xmx15G -jar /path/gear.jar comsnp --bfiles PUR HapMap --out score
- java -Xmx15G -jar /path/gear.jar propc --bfile PUR --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target
- java -Xmx15G -jar /path/gear.jar propc --bfile HapMap --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out HapMap_Ref
-~~~~~~~~~~~~~~~~~~
-
-**Example 2** generating projected pc using batch solution
+**Example 1** generating projected pc using batch solution
 ~~~~
 java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --out pur
 ~~~~
@@ -95,5 +88,18 @@
 PUR_chr1_com
 ~~~~

+The illustration of the projected pc for Puerto Ricans as well as HapMap reference is as below
+![pur](https://sourceforge.net/p/gbchen/wiki/propc/attachment/pur.png).
+
+The HapMap reference genotype data, the eigenvector scores can be found [here](http://sourceforge.net/projects/gbchen/files/Demo/proBatch.zip/download). The demo is also included.
+
+In addtion, the above procedure can also be implemented step by step if the user feels interested.
+~~~~~~~~~~~~~~~~~
+java -Xmx15G -jar /path/gear.jar comsnp --bfiles PUR HapMap --out score
+java -Xmx15G -jar /path/gear.jar propc --bfile PUR --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target
+java -Xmx15G -jar /path/gear.jar propc --bfile HapMap --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out HapMap_Ref
+~~~~~~~~~~~~~~~~~~
+
+

 [Go Homepage](https://sourceforge.net/p/gbchen/wiki/GEAR/)

propc modified by Guobo Chen

Guobo Chen — Sun, 17 May 2015 01:54:30 -0000

--- v4
+++ v5
@@ -1,17 +1,17 @@
-__Generate predicted PC__
+__Generate predicted eigenvectors__
 * * *

 **Subcommand: ** 
 propc

-Projected PC will generate principal components (PC) based on a reference population, which is the loading of PCs from.
+Projected PC will generate principal components (PC)/eigenvectors based on a reference population. 

 1. GEAR will flip the alleles to match them with the named predictor alleles. For example, when the allele coding are flipped, say A/G in the discovery panel, but coded as T/C in the validation panel, plink will leave those SNPs out. However, this option can be turn off by specifying "--auto-flip-off". 
 2. Also, plink does not take the potential risk of A/T or G/C loci, which because of their ambiguous nature, may bring in noisy in prediction. GEAR has an option --keep-atgc to use all of them or remove them.
 3. Often, the score of each SNP is provided in odds ratio format, in this circumstance, GEAR provides --logit option to transform the odds ratio to effects.
 4. It does not support dosage data, which is in MaCH format.

-In this procedure the above issues will be solved and consequently makes prediction easier.
+In this procedure the above issues will be solved and consequently makes prediction easier and avoid logistic such as strand issues.

 It should be noted that GEAR will leave out monomorphic loci if there are any.

@@ -26,45 +26,36 @@

 By default, gear assumes that the score file contains a header line. If your pc score file doesn't contains the header line, you should switch on the --no-score-header option.

-In addition, if the score can be loaded in gzip format, then --score-gz should be used instead. 
-
-**Binary genotype**
-gear propc --score scorefile.txt --bfile test --out test
-
-**MaCH dosage**
-gear propc --score scorefile.txt --mach-dosage test.mldose.gz --mach-info test.mlinfo --out test
-Or run multiple dosage distributed in multiple files
-gear propc --score scorefile.txt --mach-dosage-batch dose.txt --mach-info-batch info.txt --out test
-
-dose.txt reads like below
-mach_stage2_chr1.mldose.gz
-mach_stage2_chr2.mldose.gz
-mach_stage2_chr3.mldose.gz
-
-info.txt reads like below
-mach_stage2_chr1.mlinfo
-mach_stage2_chr2.mlinfo
-mach_stage2_chr3.mlinfo
-
-
-**Add-on options**
+**Options**
 --score
 Specify the score file.

+--batch
+Often it is better to generate projected pc for the reference samples (such as HapMap) and the target samples together. It provides more information especially in illustration, as demonstrated below.
+
+In batch.txt is the list of the roots of file names.  For examples, for two files, dat1, dat2.
+
+~~~~
+HM3_founders_noATGC_autosome_naive_imputed
+PUR_chr1_com
+~~~~
+
+The files can be more than two. By default, only consensus markers across those files will be further matched to the scores. If the user wants to generate projected pc using as many as possible markers, --greedy should switched on. However, when --greedy option is on, the generated projected PC may not be matched up at the same space.
+
 --score-gz
-Specify the score file that in in gz format.
+Specify the score file that is in gz format.

 --no-score-header
 When there is no title line for the score file, this option should be used.

 --extract-score 
-Only snps included in both --extract-score and --score/--score-gz will be used for generating profile scores.
+Only SNPs included in both --extract-score and --score/--score-gz will be used for generating profile scores.

 --remove-score 
 SNPs included in --removed-score will be used for generating profile scores.

 --keep-atgc
-It will keep AT/GC loci in the risk profile.  However, the user should confirm whether the genotypes in both discovery and the validation panels are coded on the same reference allele for each locus. 
+It will keep AT/GC loci in the risk profile. However, the user should be sure whether the genotypes in both the reference panel and the target set are coded on the same reference allele/strand for each locus. By default, this option is off.

 --auto-flip-off
 **When this option is on, a locus has flipped alleles in the testing set will not be matched.**
@@ -84,41 +75,25 @@
 **Notes**
 AT/GC loci will be left out if --keep-atgc is not on. Probably --keep-atgc should not be turned on otherwise the SNP coding on the same strand for each locus in both the discovery and the validation panels.

-When --score option is not used, the sum of the dosage score for the reference allele will be calculated.  It is equivalent to set a score file with score of 1 for each SNP.  In addition, if wants to count the sum of the specified alleles, the user can make a score file, in which the column for the reference alleles specify the reference allele and the scores are all 1. *(Deprecated)*
+In the examples below, it shows how to generate projected PC for Puerto Rican cohort in [1000 Genome projects](http://www.1000genomes.org/category/frequently-asked-questions/samples)

-**Example 1** : Generating projected pc for the target sample using HapMap as the reference sample.  
-
+**Example 1** generating projected pc for the target sample and the HapMap samples together.
 ~~~~~~~~~~~~~~~~~
- java -Xmx15G -jar /path/gear.jar propc --bfile Target --score-gz HM3_SNP.blup20.gz --out Target
-~~~~~~~~~~~~~~~~~~
-![Target PCs without reference](https://sourceforge.net/p/gbchen/wiki/propc/attachment/PCtarget.png)
-
-**Example 2** generating projected pc for the target sample and the HapMap samples together.
-
-~~~~~~~~~~~~~~~~~
- java -Xmx15G -jar /path/gear.jar comsnp --bfiles Target HapMap --out score
- java -Xmx15G -jar /path/gear.jar propc --bfile Target --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target
+ java -Xmx15G -jar /path/gear.jar comsnp --bfiles PUR HapMap --out score
+ java -Xmx15G -jar /path/gear.jar propc --bfile PUR --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target
  java -Xmx15G -jar /path/gear.jar propc --bfile HapMap --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out HapMap_Ref
 ~~~~~~~~~~~~~~~~~~

-**Example 3** One step solution
-
+**Example 2** generating projected pc using batch solution
 ~~~~
-java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --out common
-java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --greedy --out allmarker
+java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --out pur
 ~~~~

-in batch.txt is the list of the roots of file names.  For examples, two files, dat1, dat2.
-
+Inside batch.txt is
 ~~~~
-Target
-HapMap
+HM3_founders_noATGC_autosome_naive_imputed
+PUR_chr1_com
 ~~~~
-
-By default, only consensus markers across those files will be further matched to the scores.
-If --greedy is switched on, as many as possible markers will be matched to the scores.
-
-![Target PCs with reference](https://sourceforge.net/p/gbchen/wiki/propc/attachment/ProPCHapMap.png)

 [Go Homepage](https://sourceforge.net/p/gbchen/wiki/GEAR/)

propc modified by Guobo Chen

Guobo Chen — Sun, 10 May 2015 05:03:42 -0000

--- v3
+++ v4
@@ -29,12 +29,12 @@
 In addition, if the score can be loaded in gzip format, then --score-gz should be used instead.

 **Binary genotype**
-gear propc -s scorefile.txt --bfile test --out test
+gear propc --score scorefile.txt --bfile test --out test

 **MaCH dosage**
-gear propc -s scorefile.txt --mach-dosage test.mldose.gz --mach-info test.mlinfo --out test
+gear propc --score scorefile.txt --mach-dosage test.mldose.gz --mach-info test.mlinfo --out test
 Or run multiple dosage distributed in multiple files
-gear propc -s scorefile.txt --mach-dosage-batch dose.txt --mach-info-batch info.txt --out test
+gear propc --score scorefile.txt --mach-dosage-batch dose.txt --mach-info-batch info.txt --out test

 dose.txt reads like below
 mach_stage2_chr1.mldose.gz
@@ -48,6 +48,14 @@

 **Add-on options**
+--score
+Specify the score file.
+
+--score-gz
+Specify the score file that in in gz format.
+
+--no-score-header
+When there is no title line for the score file, this option should be used.

 --extract-score 
 Only snps included in both --extract-score and --score/--score-gz will be used for generating profile scores.
@@ -57,9 +65,6 @@

 --keep-atgc
 It will keep AT/GC loci in the risk profile.  However, the user should confirm whether the genotypes in both discovery and the validation panels are coded on the same reference allele for each locus. 
-
---no-score-header
-When there is no title line for the score file, this option should be used.

 --auto-flip-off
 **When this option is on, a locus has flipped alleles in the testing set will not be matched.**

propc modified by Guobo Chen

Guobo Chen — Tue, 10 Feb 2015 13:13:03 -0000

--- v2
+++ v3
@@ -95,6 +95,24 @@
  java -Xmx15G -jar /path/gear.jar propc --bfile Target --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target
  java -Xmx15G -jar /path/gear.jar propc --bfile HapMap --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out HapMap_Ref
 ~~~~~~~~~~~~~~~~~~
+
+**Example 3** One step solution
+
+~~~~
+java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --out common
+java -Xmx15G -jar /path/gear.jar probatch --batch batch.txt --score score.txt --greedy --out allmarker
+~~~~
+
+in batch.txt is the list of the roots of file names.  For examples, two files, dat1, dat2.
+
+~~~~
+Target
+HapMap
+~~~~
+
+By default, only consensus markers across those files will be further matched to the scores.
+If --greedy is switched on, as many as possible markers will be matched to the scores.
+
 ![Target PCs with reference](https://sourceforge.net/p/gbchen/wiki/propc/attachment/ProPCHapMap.png)

propc modified by Guobo Chen

Guobo Chen — Wed, 10 Dec 2014 00:24:32 -0000

--- v1
+++ v2
@@ -86,6 +86,7 @@
 ~~~~~~~~~~~~~~~~~
  java -Xmx15G -jar /path/gear.jar propc --bfile Target --score-gz HM3_SNP.blup20.gz --out Target
 ~~~~~~~~~~~~~~~~~~
+![Target PCs without reference](https://sourceforge.net/p/gbchen/wiki/propc/attachment/PCtarget.png)

 **Example 2** generating projected pc for the target sample and the HapMap samples together.

@@ -94,6 +95,7 @@
  java -Xmx15G -jar /path/gear.jar propc --bfile Target --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target
  java -Xmx15G -jar /path/gear.jar propc --bfile HapMap --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out HapMap_Ref
 ~~~~~~~~~~~~~~~~~~
+![Target PCs with reference](https://sourceforge.net/p/gbchen/wiki/propc/attachment/ProPCHapMap.png)

 [Go Homepage](https://sourceforge.net/p/gbchen/wiki/GEAR/)

propc modified by Guobo Chen

Guobo Chen — Wed, 10 Dec 2014 00:20:26 -0000

Generate predicted PC

Subcommand:
propc

Projected PC will generate principal components (PC) based on a reference population, which is the loading of PCs from.

GEAR will flip the alleles to match them with the named predictor alleles. For example, when the allele coding are flipped, say A/G in the discovery panel, but coded as T/C in the validation panel, plink will leave those SNPs out. However, this option can be turn off by specifying "--auto-flip-off".
Also, plink does not take the potential risk of A/T or G/C loci, which because of their ambiguous nature, may bring in noisy in prediction. GEAR has an option --keep-atgc to use all of them or remove them.
Often, the score of each SNP is provided in odds ratio format, in this circumstance, GEAR provides --logit option to transform the odds ratio to effects.
It does not support dosage data, which is in MaCH format.

In this procedure the above issues will be solved and consequently makes prediction easier.

It should be noted that GEAR will leave out monomorphic loci if there are any.

The format of the score pc loading file

SNP	RefAllele	pc1_score	pc2_score
SNPA	A	1.95	-0.5
SNPB	C	2.04	-0.7
SNPC	C	-0.98	0.34
SNPD	C	-0.24	3.1

By default, gear assumes that the score file contains a header line. If your pc score file doesn't contains the header line, you should switch on the --no-score-header option.

In addition, if the score can be loaded in gzip format, then --score-gz should be used instead.

Binary genotype
gear propc -s scorefile.txt --bfile test --out test

MaCH dosage
gear propc -s scorefile.txt --mach-dosage test.mldose.gz --mach-info test.mlinfo --out test
Or run multiple dosage distributed in multiple files
gear propc -s scorefile.txt --mach-dosage-batch dose.txt --mach-info-batch info.txt --out test

dose.txt reads like below
mach_stage2_chr1.mldose.gz
mach_stage2_chr2.mldose.gz
mach_stage2_chr3.mldose.gz

info.txt reads like below
mach_stage2_chr1.mlinfo
mach_stage2_chr2.mlinfo
mach_stage2_chr3.mlinfo

Add-on options

--extract-score
Only snps included in both --extract-score and --score/--score-gz will be used for generating profile scores.

--remove-score
SNPs included in --removed-score will be used for generating profile scores.

--keep-atgc
It will keep AT/GC loci in the risk profile. However, the user should confirm whether the genotypes in both discovery and the validation panels are coded on the same reference allele for each locus.

--no-score-header
When there is no title line for the score file, this option should be used.

--auto-flip-off
When this option is on, a locus has flipped alleles in the testing set will not be matched.
As genotypes may be called on the complementary strands across genotyping platforms, gear will match them by flipping SNPs automatically. For example, the named SNP is "A" in the score file, but due to flipping the reported SNPs are "T/C" in the validation set. Under --auto-flip-off option is switched off, gear will flip "T/C" back to "A/G", and consequently match the score to the validation set. Of course, gear presumes the polymorphism is same across the discovery and the validation sets.

There are four possible schemes for matching a SNP between the discovery and the validation sets

Scheme
The named score SNP matches the reference allele in the validation set
The named score SNP matches the alternative allele in the validation set
The named score SNP matches the flipped reference allele in the validation set
The named score SNP matches the flipped alternative allele in the validation set
Matches neither, then this locus will be discarded

Notes
AT/GC loci will be left out if --keep-atgc is not on. Probably --keep-atgc should not be turned on otherwise the SNP coding on the same strand for each locus in both the discovery and the validation panels.

When --score option is not used, the sum of the dosage score for the reference allele will be calculated. It is equivalent to set a score file with score of 1 for each SNP. In addition, if wants to count the sum of the specified alleles, the user can make a score file, in which the column for the reference alleles specify the reference allele and the scores are all 1. (Deprecated)

Example 1 : Generating projected pc for the target sample using HapMap as the reference sample.

 java -Xmx15G -jar /path/gear.jar propc --bfile Target --score-gz HM3_SNP.blup20.gz --out Target

Example 2 generating projected pc for the target sample and the HapMap samples together.

 java -Xmx15G -jar /path/gear.jar comsnp --bfiles Target HapMap --out score
 java -Xmx15G -jar /path/gear.jar propc --bfile Target --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out Target
 java -Xmx15G -jar /path/gear.jar propc --bfile HapMap --extract-score score.comsnp --score-gz HM3_SNP.blup20.gz --out HapMap_Ref

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