proximalAdjByCleanUpdTSeq: adjust the proximal CP sites by cleanUpdTseq

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

Description

adjust the proximal CP sites by cleanUpdTseq

Usage

proximalAdjByCleanUpdTSeq(idx.list, cov_diff.list, seqnames, starts, strands, 
                        genome, classifier, classifier_cutoff, 
                        shift_range, search_point_START, step=1)

Arguments

idx.list	the offset of positions of CP sites
cov_diff.list	the SSE values
seqnames	sequence names
starts	starts
strands	strands
genome	a BSgenome object
classifier	cleanUpdTSeq classifier
classifier_cutoff	cutoff value of the classiffier
shift_range	the searching range for the better CP sites
search_point_START	just in case there is no better CP sites
step	adjust step, default 1, means adjust by each base by cleanUpdTSeq.

Details

the step for calculating is 10, can not do every base base it is really very slow.

Value

the offset of positions of CP sites after filter

Author(s)

Jianhong Ou

See Also

proximalAdjByPWM, proximalAdj, PAscore2

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