diff rDiff/src/configure_rdiff.m @ 0:0f80a5141704

version 0.3 uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/src/configure_rdiff.m	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,141 @@
+function CFG = configure_rdiff(CFG)
+% configure_rdiff(CFG)
+
+%%% rDiff parameters %%%
+
+% Give the filenames of the bam-files to be considered
+CFG.BAM_FILES={'condition_A_replicate_1.bam','condition_A_replicate_2.bam','condition_B_replicate_1.bam','condition_B_replicate_2.bam'};
+
+%Name of the experiment. Use the FILENAMES if the entries are empty.
+CFG.NAMES={'A1','A2','B1','B2'};
+
+
+% Give the directory where the bam-files are
+CFG.data_dir = '' ;
+
+% Indicate to which sample the bam-files belong
+CFG.SAMPLES=[1,1,2,2];
+
+% Location of the gene structure
+CFG.genes_path='' ;
+
+% Output directory
+CFG.out_base =  '' ;
+
+% Output directory for temporary files
+CFG.out_base_temp =  '' ;
+
+%Length of the reads
+CFG.sequenced_length=75;
+
+% Prefix for the chromosome name when getting geetting reads from
+% the bam-files
+CFG.chr_prefix='';
+
+%%% Read filters %%%
+
+% Minimal read length
+CFG.min_read_length=30;
+
+
+
+%%% Parameters for gene expression estimation
+%Count the number of reads ( CFG.estimate_gene_expression=1 for yes
+%give the Files for the expresison in CFG.GENE_EXPR_FILES
+CFG.estimate_gene_expression=1;
+
+% Use the following files in CFG.GENE_EXPR_FILES for the
+% gene_expression. Those must be Tab-delimitered files where each
+% line contains the gene name folowed by the expressiob
+CFG.Counts_gene_expression='';
+CFG.Counts_rDiff_parametric='';
+CFG.Counts_rDiff_nonparametric='';
+
+
+
+%%% Parameters for variance function
+
+% Use a parametric form for the variance function for sample 1: sigma= a + bx + cx^2
+% (CFG.predefined_variance_function1=[] if not; CFG.predefined_variance_function1=[a,b,c] otherwise)
+% If CFG.predefined_variance_function1=[a,b,c] is given, the other
+% parameters for the variance function estimations are ignored for
+% sample 1
+CFG.predefined_variance_function1=[];
+
+% Use a parametric form for the variance function for sample 2: sigma= a + bx + cx^2
+% (CFG.predefined_variance_function2=[] if not; CFG.predefined_variance_function2=[a,b,c] otherwise)
+% If CFG.predefined_variance_function2=[a,b,c] is given, the other
+% parameters for the variance function estimations are ignored 
+% for sample 2
+CFG.predefined_variance_function2=[];
+
+% compute variance function for sample 1 ( 1 = yes , 0 = use precomputed
+% variance function saved under CFG.variance_function_1) 
+CFG.compute_variance_function_1=1;
+CFG.variance_function_1='';
+CFG.save_variance_function_1='variance_function_1.mat';
+
+% compute variance function for sample 2 ( 1 = yes , 0 = use precomputed
+% variance function saved under CFG.variance_function2) 
+CFG.compute_variance_function_2=1;
+CFG.variance_function_2='';
+CFG.save_variance_function_2='variance_function_2.mat';
+
+% subsample points for the variance function estimate for rDiff.nonparametric
+CFG.rDiff_nonparametric_subsample_variance_estimation=10000;	
+
+% Subsample the mean-variance pairs to increas the speed of the
+% local regression.CFG.variance_samplebins is the number of bins to
+% use and CFG.variance_samples_per_bin is how many samples should
+% be drwan per bin
+CFG.variance_samplebins=100;
+CFG.variance_samples_per_bin=500;
+
+
+
+%%% Testing parameters %%%
+
+% subsample reads down to rDiff.subsample to increase speed ( If no
+% subsampling shall be done set CFG.rDiff_subsample to 0
+CFG.rDiff_subsample=10000;
+
+% Clib the first CFG.bases_to_clip bases at the end of the reads
+CFG.bases_to_clip=3;
+
+%Number of bootraps for nonparametric test
+CFG.bootstraps=1000;
+
+%Number of bins for variance matching
+CFG.nr_of_slices=10;
+
+% Tests to perform
+CFG.perform_nonparametric=0;
+CFG.perform_parametric=0;
+CFG.perform_mmd=0;
+CFG.perform_poisson=0;
+
+
+%%%%% rproc settings %%%%%
+CFG.use_rproc = 0; % 1: cluster submission or 0: locally
+if CFG.use_rproc,
+    CFG.rproc_num_jobs              = 100;
+    CFG.rproc_memreq                = 8000;
+    CFG.rproc_par.priority          = 55;
+    CFG.rproc_par.resubmit          = 3;
+    CFG.rproc_par.mem_req_resubmit  = [ 24000 40000 60000];
+    CFG.rproc_par.time_req_resubmit = [60*60 100*60 90*60];
+    CFG.rproc_par.express           = 0;
+    CFG.rproc_par.immediately_bg    = 0;
+    CFG.rproc_par.immediately       = 0;
+    CFG.rproc_par.arch              = 64;
+    CFG.rproc_par.identifier        = '';
+    CFG.rproc_par.verbosity         = 0;
+    CFG.rproc_time                  = 15*60; % mins
+else
+    CFG.rproc_num_jobs              = 1;
+end
+
+
+
+
+