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Expected_Results 2016-04-19
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ReadMe.txt 2016-04-12 1.3 kB
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chrTable_example.txt 2016-04-12 445 Bytes
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gapfile_example.txt 2016-04-12 43.1 kB
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regionTable_example.txt 2016-04-12 62 Bytes
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# README

# instructions on how to run test for InvertR Strand-seq analysis package
# available at https://sourceforge.net/projects/strandseq-invertr/files/testData/
# Ashley D. Sanders
 
# 1. install and load 'InvertR' library (https://github.com/drashley/InvertR.git)
# 2. load test files:
    chrTable <-read.table('./chrTable_example.txt')
    gapfile <- read.table('./gapfile_example.txt')
    roiList <-read.table('./regionTable_example.txt')
# 3. run examples A to C in directory containing BAM files (if directory contains BED files, change: type='bed')
  


# Example A. visualize chromosome 22 without any filtering:
      
runInvertR(chrTable[22,], 
           type='bam', 
           dataDirectory="./exampleA/",
           bin=1000,
           gapfile=0,
           WCcutoff=0,
           findROIs=F)
 


# Example B. analyze all 'ww' or 'cc' chromosomes, and predict ROIs
 
runInvertR(chrTable,
           type='bam',
           dataDirectory="./exampleB/",
           bin=1000,
           gapfile=gapfile)
 


# Example C. analyze an ROIfile with defined coordinates, and test a smaller bin

runInvertR(roiList,
           type='bam',
           dataDirectory="./exampleC/",
           bin=50,
           ROI=T,
           padding=20000,
           WCcutoff=0)
Source: ReadMe.txt, updated 2016-04-12