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Data_sample.txt
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# Data sample file
# This is a comment line
// This is also a comment line
// ./rjmcmc [Dataname] stepnumber
// All variables should be capitalized
// All white spaces can be space or tab or return
// Also blank lines are tolerated
// Real data from Wei Huang
// File generated by Xiaoyi Cao 2012/1/31
// Define the number of timepoints in the analysis
TIMEPOINTS 3
// Define the number of genes in the analysis
GENES 23
// Define the total number of samples (across all timepoints)
TOTAL_SAMPLES 53
// Define the number of samples for every time point
// The number of values after the name should be the same as TIMEPOINTS
SAMPLES_BY_TIME
3 20 30
// Define K0 and K1, please refer to the paper for a proper value
K0 0.04
K1 0.8
// Whether a forest will be built for the analysis, TRUE/FALSE
BUILD_FOREST FALSE
// All the data need to be following DATA
// The number of data points should be the same as
// (number of genes) x (number of samples in total)
// Notice that Data should be ordered as the following:
// <gene 0 for sample 0 at time 0> <gene 1 for sample 0 at time 0> ... <gene n for sample 0 at time 0>
// <gene 0 for sample 1 at time 0> <gene 1 for sample 1 at time 0> ...
// ...
// <gene 0 for sample 0 at time 1> <gene 1 for sample 0 at time 1> ... <gene n for sample 0 at time 1>
// ...
// <gene n for sample s at time t>
DATA
6.41081250421216 4.52267591369281 7.42864161698442 -0.762461409942201 -0.912819641170862 -0.636264461344968 -0.299646597930297 0.259027095107334 -0.388895363693282 -1.70862016442551 0.880584640508815 -0.193554514368295 1.2813597295683 0.349938685801879 0.669851440979655 0.238174499990595 0.823032237939537 -0.17129275358075 1.21065984905087 -0.294525736111999 0.672101671851317 -0.592913417884721 0.787661227944272
3.15547003022851 5.7176337032488 2.84653736656801 0.806524743045684 1.48021061362574 -1.02134396776522 0.485387104480494 -1.37804103198544 -0.572135650684954 0.371109809180493 -2.1973427598465 1.35832067210594 -2.04462606500643 -0.935971563824482 -0.00800757272561434 -0.896915660456582 0.403778214421763 1.27267006650061 1.54806525118127 1.71168931423066 0.711203640006366 -0.863331877576264 -0.937729751188251
7.09618620462395 3.31643618636172 2.08975317544429 -1.07788827469996 0.328048914517249 0.0957732373611841 0.990984124335969 -0.986377486474095 -0.00891385432090604 -0.214250152239316 -0.806796846634536 -0.680894364802703 -0.784393649044454 0.78064424931 -0.820603550879615 0.233002817105277 0.000823418608398739 0.91865401099776 -0.146421745788296 -1.75698361131823 0.657723338028899 0.72242241608929 1.82168208703383
6.12368514067893 3.84832421782104 4.06228333306353 1.08218600339555 -0.305265706138951 -0.257322779069448 -1.23701211050892 0.929903573460267 -1.8122571151875 0.411722394879925 -1.19523530667325 -0.431688878805149 -0.859575784627579 -1.90442930984605 1.26636177393652 -0.904292408199166 -0.218509904189065 0.180617100497144 -0.63519842138891 1.2780722904027 -1.19468799286838 0.758825088012835 -1.93911508163244
4.07287691116368 6.38928322006553 2.74755818956366 -2.44756169437615 0.688556265165295 0.6003834384564 0.537264035742147 -0.439521512649527 0.312035665537193 0.503082941541594 0.623168691812548 -1.75785104557125 0.00495714678292793 -0.549553696859029 1.4448768125277 0.500016006184749 -0.288241282670188 -0.446354008393161 1.02704274649288 -0.0670252751847264 0.518385030485039 -0.714240020469686 0.0487877308680158
5.06368513602252 5.72894918831525 6.2600864378107 0.0085075552089208 0.119137689191012 -1.13460659153032 -0.677314052603462 0.523771271823665 0.647865065138174 -1.31989602807185 0.867297579379423 0.270966369079807 1.6082626201825 0.426945099706716 -0.223126507101355 1.88835266333482 -1.57453944449479 -1.04301676995527 -0.0652220125946662 -0.0091605792522689 0.186378072341285 -0.612945876144436 0.799937765351751
6.25752494882533 4.26748201808824 4.12804144232555 1.00571955458448 1.40979444837582 1.04067537946465 0.644996238926747 2.15267200211194 -1.76493055801146 -0.450266078543787 0.071951550672692 -1.09672563133509 0.244820235665596 1.03488178701253 1.15086416406631 2.40867984145806 0.227080003879815 0.459938207109453 0.282779816719684 -0.0362551888405088 -1.09466403520586 -0.967706453904246 -0.527586456075449
4.88627863987505 5.20667010092837 4.47450669995455 -0.104540344542841 -0.927563728849991 -0.168461247881654 1.55465643773844 -1.78806788686355 -1.29159710059417 -0.320744478183243 1.2193715568136 -1.5731913390678 -0.463570379753388 -0.469552950719555 0.772110322278701 -1.20388974205473 -0.659672857187402 0.514376819117375 1.3921284053817 -0.384238834103969 0.0421223537027057 0.296567406738439 -0.49150782573951
6.24988342257343 2.60669197740512 5.13765149828746 -1.62916063220853 0.875237004340179 0.762735153182465 -0.865660704954919 -0.367053727056558 -0.346344489593795 -0.571744759493974 1.32825880504633 0.523355935510669 0.123692320108932 0.0862699550905879 -0.215110277624759 -1.47338562866724 -1.37224534066875 -0.593672936174125 0.960608844771374 -0.198906618126106 0.00234493790465103 0.346179742935458 -0.534184512643023
4.02185624929782 5.83473192542204 5.82545051813496 0.0433638578018901 -0.413025297366648 1.0805462431874 1.17714400741865 0.914793798390527 -2.18854837480801 -1.15000181283863 -0.320834832796519 0.721070278313098 0.413027893400789 -0.410329539643892 2.23602146358511 0.9428339889841 0.612851610160838 -0.509882068948278 -0.845577998850547 2.51067879359473 0.931645156674214 -0.551688858535586 -0.5482185828421
4.85963037688797 5.59849176197247 4.2616785258514 0.362007232757603 1.24083292728231 -0.461468957942565 -1.05609915254088 0.971225553044219 0.268279252653927 0.378341817594848 1.19976336091592 0.518337359749853 -1.59972260400604 1.84452423235759 -0.998615828984461 -0.011291951374539 -0.288494747717377 -0.157778624118945 0.476015468985158 -0.0822402024303726 0.287641893780326 0.0901464488315315 -0.238245976162993
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// Whether you would like to monitor the weight of the cluster that a specific sample belongs to
// The value should be provided in pairs
// The first value is timepoint (0-based), the second one is the sample index (0-based)
// The following line will generate weight tracing values for:
// sample 2 at time 0
// sample 5 at time 1 and
// sample 5 at time 2
//WEIGHT_MONITOR 0 2 1 5 2 5
END // This is optional