[Genabel-commits] r1166 - pkg/OmicABEL/src/reshuffle

[noreply at r-forge.r-project.org]

Author: yurii
Date: 2013-03-20 09:48:03 +0100 (Wed, 20 Mar 2013)
New Revision: 1166

Removed:
   pkg/OmicABEL/src/reshuffle/README.txt
Log:
deleting reshuffle's README from src/reshuffle (now only the copy in doc, README-reshuffle, is there)

Deleted: pkg/OmicABEL/src/reshuffle/README.txt
===================================================================
--- pkg/OmicABEL/src/reshuffle/README.txt	2013-03-19 20:23:53 UTC (rev 1165)
+++ pkg/OmicABEL/src/reshuffle/README.txt	2013-03-20 08:48:03 UTC (rev 1166)
@@ -1,79 +0,0 @@
-Reshuffle ver 0.000
-
-Parameters:
-
-For the first it should be file name without iout and out extensions:
-	(--B_eigen_1000) 
-	if your files are B_eigen.iout and B_eigen.out
-
-Data dimensions 
-	(--datadims)  Gives back t, m, p
-output: "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"
-
-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
-	
-Info 
-	(--info) write some information about programm'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
-
-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