[Genabel-commits] r1417 - in pkg/OmicABEL: doc src/reshuffle
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 26 20:23:54 CET 2013
Author: sharapovsodbo
Date: 2013-11-26 20:23:54 +0100 (Tue, 26 Nov 2013)
New Revision: 1417
Modified:
pkg/OmicABEL/doc/README-reshuffle
pkg/OmicABEL/src/reshuffle/makefile
Log:
-ver 0.32
--upd: documentation: README-reshuffle
Modified: pkg/OmicABEL/doc/README-reshuffle
===================================================================
--- pkg/OmicABEL/doc/README-reshuffle 2013-11-22 14:32:58 UTC (rev 1416)
+++ pkg/OmicABEL/doc/README-reshuffle 2013-11-26 19:23:54 UTC (rev 1417)
@@ -1,88 +1,99 @@
-Reshuffle ver 0.000
+reshuffle ver 0.031
-Parameters:
+Parameters:
The first parameter tells the name of CLACK-GWAS output file (without iout
and out extensions), for example, the first parameter must be
- B_myeigen
+ B_myeigen
-if CLAK-GWAS output files are B_myeigen.iout and B_myeigen.out
+if CLAK-GWAS output files are B_myeigen.iout and B_myeigen.out
A number of options allow to extract different types of information from
CLAK-GWAS outputs.
Data dimensions are obtained by adding option
- --datadims
-
+ --datadims
+default_output: "datadims.txt"
which gives back t (number of traits), m (number of markers), p (number of
-covariates + 2); the information is stored in a file named "datadims.txt"
+covariates + 2); the information is stored in a file named "datadims.txt"
-SNP names
- default: (--snpnames) : all
- by index (--snpnames=27) : name of snp#27
- by index range, combination (--snpnames=27,2-12,4-20) : name of snp #2-20,27
-output: "snpnames.txt"
-
-Trait names
- default (--traitnames): all
- by index (--traitnames=27) : name of trait #27
- by index range, combination (--traitnames=27,2-12,15)
-output: "traitnames.txt"
+Extract SNP names:
-Heritabilities, sigma, res_sigma, estimates
- Default: (--heritabilities) : all traits
- Reange,indexes (--heritabilities=1-10,4,5-12) : for traits #1-12
- trait's names (--heritabilities=hgta,hdla) : for traits hgta,hdla
- regexp in trait's names (--heritabilities=regexp=t) : for traits, in the start of which is "t" : tga,tca (in data_4test)
- all combinations (--heritabilities=1-10,4,5-12,hgta,lipid_tca,regexp=lipid_)
-output: "estimates.txt"
-Results - association
- by SNP
- Dafault (--snp) : for all snp for all traits
- indexes, ranges (--snp=12,100-1000,500-10000,22000) : for all traits
- names (--snp=rs3121561,rs6687776) : for snps rs3121561,rs6687776
- names+around (--snp=rs3121561,rs6687776,before=10,after=15)
- for (-10,9,...,-1,rs3121561,1,2,...,15,16) + (-10,9,...,-1,rs6687776,1,2,...,15,16)
- indexes+names+focus (--snp=1-20,50,rs3121561,rs6687776,before=10,after=15)
- for snps : #1-20,50 + (-10,9,...,-1,rs324001,1,2,...,15,16) + (-10,9,...,-1,rs123123,1,2,...,15,16)
- NB!: focus only for snp's names, not for indexes
- output: "data.txt"
- by trait
- Dafault (--trait) : for all snp for all traits
- indexes,range (--trait=1-10,12) : for snp #12 for all traits
- by names (--traits=tca,hdla) : for traits tca,hdla
- regexp in trait's names (traits=regexp=lipids_) : for all traits, which name in the beginig has "lipids_"
- all combinations
- output: "data.txt"
- Chi2 more than some threshold
- (--chi=20) for snps,which chi>20 for all traits
- output: "chi_data.txt"
- All combinations of traits,snps, Chi2
- (--traits=1-2--snps=1-1000--chi=15) for traits #1-2 for snps#1-1000, which chi>15
- output: "chi_data.txt"
-
-Just write data with chi
- (--chi) : write data(with chi column) for all snps for all traits
- all combinations are supported
- output: "chi_data.txt"
-Dataslim
- Creating a sub-matrix by Chi2>X (--chi=X--dataslim)
- output: "slim_data.txt"
-
-Test
- (--test) run all tests
- output: test.txt
-
+ default: (--snpnames) : all
+ by index (--snpnames=27) : name of snp#27
+ by index range, combination (--snpnames=27,2-12,4-20) : name of snp #2-20,27
+default_output: "snpnames.txt"
+
+Extract trait names:
+
+ default (--traitnames): all
+ by index (--traitnames=27) : name of trait #27
+ by index range, combination (--traitnames=27,2-12,15)
+default_output: "traitnames.txt"
+
+Extract heritabilities, sigma, res_sigma, estimates:
+
+ Default: (--herit) : all traits
+ Range,indexes (--herit=1-10,4,5-12) : for traits #1-12
+ trait's names (--herit=hgta,hdla) : for traits hgta,hdla
+ reg-exp in trait's names (--herit=reg-exp=t) : for traits, in the start of which
+ is "t" : tga,tca (in data_4test)
+ all combinations (--heritabilities=1-10,4,5-12,hgta,lipid_tca,reg-exp=lipid_)
+default_output: "estimates.txt"
+
+Extract results for association:
+ by SNP
+ Default (--snp) : for all snp for all traits
+ indexes, ranges (--snp=12,100-1000,500-10000,22000) : for all traits
+ names (--snp=rs3121561,rs6687776) : for snps rs3121561,rs6687776
+ names+around (--snp=rs3121561,rs6687776,before=10,after=15)
+ for (-10,9,...,-1,rs3121561,1,2,...,15,16) + (-10,9,...,-1,rs6687776,1,2,...,15,16)
+ indexes+names+focus (--snp=1-20,50,rs3121561,rs6687776,before=10,after=15)
+ for snps : #1-20,50 + (-10,9,...,-1,rs324001,1,2,...,15,16) + (-10,9,...,-1,rs123123,1,2,...,15,16)
+ NB!: focus only for snp's names, not for indexes
+ default_output: "data.txt"
+
+ by trait
+
+ Default (--trait) : for all snp for all traits
+ indexes,range (--trait=1-10,12) : for snp #12 for all traits
+ by names (--traits=tca,hdla) : for traits tca,hdla
+ reg-exp in trait's names (traits=reg-exp=lipids_) : for all traits, which name
+ in the beginning has "lipids_"
+ all combinations are supported
+ default_output: "data.txt"
+
+ Chi2 more than some threshold
+ (--chi) for write data with column "Chi2", which contains chi-square
+ (--chi=20) for snps,which chi>20 for all traits
+ default_output: "data_chi.txt"
+
+ All combinations of traits,snps, Chi2
+ (--traits=1-2--snps=1-1000--chi=15): for traits #1-2 for snps#1-1000, which chi>15
+ default_output: "data_chi.txt"
+
+
+Dataslim
+
+ Creating a sub-matrix by Chi2>X
+ (--chi=X --dataslim)
+ In this case reshuffle screens chi-squares for all pairs trait-SNP. If pair trait_1 - SNP_1
+ has chi-square over than X, reshuffle adds trait in TRAIT_LIST and SNP_1 in SNP_LIST.
+ After screening ends, reshuffle extract results for traits in TRAIT_LIST and SNP_LIST.
+ This makes output file much smaller!
+ default_output: "slim_data.txt"
+
Info
- (--info) write some information about programm's run
+ (--info) write some information about program’s run
-Examples:
-Reshuffle.exe B_1112_NA_clear_RNA_nocovar --traitnames=1-4,1--snpnames=1-10,20-30,46--traits=1--snps=1-100
+Examples:
-outputs from B_1112_NA_clear_RNA_nocovar.iout and B_1112_NA_clear_RNA_nocovar.out:
+reshuffle B_1112_NA_clear_RNA_nocovar --traitnames=1-4,1--snpnames=1-10,20-30,46--traits=1--snps=1-100
- traitnames.txt : with trait's names hgta,tga,tca,ldla
- snpnames.txt Names of snps #1-10,20-30,46
+outputs from B_1112_NA_clear_RNA_nocovar.iout and B_1112_NA_clear_RNA_nocovar.out:
+
+ traitnames.txt : with trait's names hgta,tga,tca,ldla
+ snpnames.txt Names of snps #1-10,20-30,46
trait_hgta.txt : result of association for trait "hgta" for snps #1-100
\ No newline at end of file
Modified: pkg/OmicABEL/src/reshuffle/makefile
===================================================================
--- pkg/OmicABEL/src/reshuffle/makefile 2013-11-22 14:32:58 UTC (rev 1416)
+++ pkg/OmicABEL/src/reshuffle/makefile 2013-11-26 19:23:54 UTC (rev 1417)
@@ -1,14 +1,14 @@
all:
- g++ -O3 -Wall -c -fmessage-length=0 -o iout_file.o "D:\Work\SVNRepository\OmicABEL\src\reshuffle\iout_file.cpp"
- g++ -O3 -Wall -c -fmessage-length=0 -o reshuffle.o "D:\Work\SVNRepository\OmicABEL\src\reshuffle\reshuffle.cpp"
- g++ -O3 -Wall -c -fmessage-length=0 -o Parameters.o "D:\Work\SVNRepository\OmicABEL\src\reshuffle\Parameters.cpp"
- g++ -O3 -Wall -c -fmessage-length=0 -o main.o "D:\Work\SVNRepository\OmicABEL\src\reshuffle\main.cpp"
- g++ -o Reshuffle.exe "reshuffle.o" "main.o" "iout_file.o" "Parameters.o"
-
+ g++ -O3 -Wall -c -fmessage-length=0 -o iout_file.o iout_file.cpp
+ g++ -O3 -Wall -c -fmessage-length=0 -o reshuffle_obj.o reshuffle.cpp
+ g++ -O3 -Wall -c -fmessage-length=0 -o Parameters.o Parameters.cpp
+ g++ -O3 -Wall -c -fmessage-length=0 -o main.o main.cpp
+ g++ -o reshuffle "reshuffle_obj.o" "main.o" "iout_file.o" "Parameters.o
+
clean:
del iout_file.o
- del reshuffle.o
+ del reshuffle_obj.o
del Parameters.o
del main.o
- del Reshuffle.exe
\ No newline at end of file
+ del reshuffle
\ No newline at end of file
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