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comparison ideas.R @ 181:475fa65d5138 draft

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author greg
date Thu, 01 Feb 2018 12:54:15 -0500
parents f32f15562a82
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180:15bd502e6a0c 181:475fa65d5138
8 make_option(c("--bychr"), action="store_true", dest="bychr", default=FALSE, help="Output chromosomes in separate files"), 8 make_option(c("--bychr"), action="store_true", dest="bychr", default=FALSE, help="Output chromosomes in separate files"),
9 make_option(c("--chrom_bed_input"), action="store", dest="chrom_bed_input", default=NULL, help="Chromosome windows positions file"), 9 make_option(c("--chrom_bed_input"), action="store", dest="chrom_bed_input", default=NULL, help="Chromosome windows positions file"),
10 make_option(c("--chromosome_windows"), action="store", dest="chromosome_windows", default=NULL, help="Windows positions by chroms config file"), 10 make_option(c("--chromosome_windows"), action="store", dest="chromosome_windows", default=NULL, help="Windows positions by chroms config file"),
11 make_option(c("--hp"), action="store_true", dest="hp", default=FALSE, help="Discourage state transition across chromosomes"), 11 make_option(c("--hp"), action="store_true", dest="hp", default=FALSE, help="Discourage state transition across chromosomes"),
12 make_option(c("--initial_states"), action="store", dest="initial_states", type="integer", default=NULL, help="Initial number of states"), 12 make_option(c("--initial_states"), action="store", dest="initial_states", type="integer", default=NULL, help="Initial number of states"),
13 make_option(c("--input_files_path"), action="store", dest="input_files_path", help="IdeasPre input dataset extra files path"),
14 make_option(c("--ideas_input_config"), action="store", dest="ideas_input_config", help="IDEAS_input_config file"), 13 make_option(c("--ideas_input_config"), action="store", dest="ideas_input_config", help="IDEAS_input_config file"),
15 make_option(c("--log2"), action="store", dest="log2", type="double", default=NULL, help="log2 transformation"), 14 make_option(c("--log2"), action="store", dest="log2", type="double", default=NULL, help="log2 transformation"),
16 make_option(c("--maxerr"), action="store", dest="maxerr", type="double", default=NULL, help="Maximum standard deviation for the emission Gaussian distribution"), 15 make_option(c("--maxerr"), action="store", dest="maxerr", type="double", default=NULL, help="Maximum standard deviation for the emission Gaussian distribution"),
17 make_option(c("--max_cell_type_clusters"), action="store", dest="max_cell_type_clusters", type="integer", default=NULL, help="Maximum number of cell type clusters allowed"), 16 make_option(c("--max_cell_type_clusters"), action="store", dest="max_cell_type_clusters", type="integer", default=NULL, help="Maximum number of cell type clusters allowed"),
18 make_option(c("--max_position_classes"), action="store", dest="max_position_classes", type="integer", default=NULL, help="Maximum number of position classes to be inferred"), 17 make_option(c("--max_position_classes"), action="store", dest="max_position_classes", type="integer", default=NULL, help="Maximum number of position classes to be inferred"),