InPAS (version 1.4.4)

CPsite_estimation: 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

utr3

output of utr3Annotaion

MINSIZE

min size of short form

window_size

window size

search_point_START

search start point

search_point_END

search end point

cutStart

cut from start

cutEnd

cut from end

adjust_distal_polyA_end

adjust distal site or not

background

how to get the local background

z2s

output of zScoreThrethold

coverage_threshold

cutoff value for coverage

long_coverage_threshold

cutoff value for long form

PolyA_PWM

polyA PWM

classifier

classifier

classifier_cutoff

classifier cutoff

shift_range

shift range

depth.weight

output of depthWeight

genome

a BSgenome object

tmpfolder

temp folder could save and reload the analysis data for resume analysis.

silence

report progress or not. default not report.

Value

a data.frame

See Also

CPsites, searchProximalCPs, proximalAdj, proximalAdjByPWM, proximalAdjByCleanUpdTSeq, PAscore,PAscore2