CPsite_estimation: estimate the cpsites

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

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, step=1, two_way=FALSE,
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
step	adjust step, default 1, means adjust by each base by cleanUpdTSeq.
two_way	Search the proximal site from both direction or not.
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

Author(s)

Jianhong Ou

See Also

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

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.