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Last data update: 2014.03.03
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R: estimate the cpsites
| CPsite_estimation | R Documentation |
estimate the cpsites
Description
estimate the cpsites for a giving chromosome
Usage
CPsite_estimation(chr.cov, utr3, MINSIZE, window_size, search_point_START,
search_point_END, cutStart, cutEnd, adjust_distal_polyA_end,
background, z2s, coverage_threshold, long_coverage_threshold,
PolyA_PWM, classifier, classifier_cutoff, shift_range,
depth.weight, genome,
tmpfolder=NULL, silence=TRUE)
Arguments
chr.cov |
coverage list for one chromosome
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utr3 |
output of utr3Annotaion
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MINSIZE |
min size of short form
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window_size |
window size
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search_point_START |
search start point
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search_point_END |
search end point
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cutStart |
cut from start
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cutEnd |
cut from end
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adjust_distal_polyA_end |
adjust distal site or not
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background |
how to get the local background
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z2s |
output of zScoreThrethold
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coverage_threshold |
cutoff value for coverage
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long_coverage_threshold |
cutoff value for long form
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PolyA_PWM |
polyA PWM
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classifier |
classifier
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classifier_cutoff |
classifier cutoff
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shift_range |
shift range
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depth.weight |
output of depthWeight
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genome |
a BSgenome object
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tmpfolder |
temp folder could save and reload the analysis data for resume analysis.
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silence |
report progress or not. default not report.
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Value
a data.frame
Author(s)
Jianhong Ou
See Also
CPsites, searchProximalCPs,
proximalAdj,
proximalAdjByPWM, proximalAdjByCleanUpdTSeq,
PAscore,PAscore2
Results
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providing 
.