Mercurial > repos > stemcellcommons > spp_tool

comparison run_spp.R @ 1:23b22c1692fa draft default tip

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author hackdna
date Tue, 20 May 2014 10:53:35 -0400
parents b15734276ca3
children
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0:b15734276ca3 1:23b22c1692fa
118 sep.max <- 600 # max strand shift 118 sep.max <- 600 # max strand shift
119 sep.bin <- 5 # increment for strand shift 119 sep.bin <- 5 # increment for strand shift
120 sep.peak <- NA # user-defined peak shift 120 sep.peak <- NA # user-defined peak shift
121 exclude.min <- 10 # lowerbound of strand shift exclusion region 121 exclude.min <- 10 # lowerbound of strand shift exclusion region
122 exclude.max <- NaN # upperbound of strand shift exclusion region 122 exclude.max <- NaN # upperbound of strand shift exclusion region
123 n.nodes <- NA # number of parallel processing nodes 123 n.nodes <- 32 # number of parallel processing nodes
124 fdr <- 0.01 # false discovery rate threshold for peak calling 124 fdr <- 0.01 # false discovery rate threshold for peak calling
125 npeak <- NA # threshold on number of peaks to call 125 npeak <- NA # threshold on number of peaks to call
126 temp.dir <- tempdir() # temporary directory 126 temp.dir <- tempdir() # temporary directory
127 chrname.rm.pattern <- NA # chromosome name pattern used to remove tags 127 chrname.rm.pattern <- NA # chromosome name pattern used to remove tags
128 output.odir <- NA # Output directory name 128 output.odir <- NA # Output directory name