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# TileMap Parameter Settings #
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# Step O: Working Directory  #
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O.1-[Working directory] = C:\Projects\research_harvard\affy_project\analysis\tiling_paper\
O.2-[Project Title] = cMycA_tile

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# Step I: Probe Summary      #
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I.1-[Compute probe level test-statistics?] (1:yes; 0:no) = 0
I.2-[Raw data file] = cMycA_tile_I_f_pb.sum
I.3-[Range of test-statistics] (0: default; 1: [0,1], 2: (-inf, +inf)) = 1
I.4-[Zero cut] = 1e-4

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# Step II: Repeat Filtering  #
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II.1-[Apply local repeat filter?] (0:No; 1:Yes) = 0
II.2-[*.refmask file] = P1_CHIP_A.Anti-Sense.hs.NCBIv33.sary.bpmap.refmask

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# Step III: Region Summary   #
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III.1-[Combine neighboring probes?] (0:No; 1:Yes) = 1
III.2-[Method to combine neighboring probes] (0:HMM, 1:MA) = 1

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# Step IV: HMM               #
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IV.1-[Posterior probability >] = 0.5
IV.2-[Maximal gap allowed] = 1000
IV.3-[Method to set HMM parameters] (0:UMS, 1:Set by users) = 0

IV.4-[Provide your own selection statistics?] (0: No, use default; 1: Yes) = 0
IV.5-[If Yes to IV.4, selection statistics file] = cMycA_tile_I_f.pbsum
IV.6-[G0 Selection Criteria, p%] = 0.01
IV.7-[G1 Selection Criteria, q%] = 0.05
IV.8-[Selection Offset] = 1
IV.9-[Grid Size] = 1000
IV.10-[Expected hybridization length] = 28

IV.11-[Path to transition probability matrix] = cMycA_tile_transp.txt
IV.12-[Path to emission probability matrix] = cMycA_tile_emissp.txt

##############################
# Step V: Moving Average     #
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V.1-[Local FDR <] = 0.5
V.2-[Maximal gap allowed] = 500
V.3-[W] = 5
V.4-[Method to compute local FDR] (0:UMS; 1:Permutation Test) = 0

V.5-[Provide your own selection statistics?] (0: No, use default; 1: Yes) = 0
V.6-[If Yes to IV.4, selection statistics file] = cMycA_tile_I_f.pbsum
V.7-[G0 Selection Criteria, p%] = 0.01
V.8-[G1 Selection Criteria, q%] = 0.05
V.9-[Selection Offset] = 6

V.10-[Grid Size] = 1000