polish_CPs: polish the searching results of CP sites

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

polish the searching results of CP sites

Description

remove the multiple positions of CP sites for the same 3' UTRs and only keep the best CP sites for proximal and distal.

Usage

polish_CPs(CPs, output.all, DIST2END = 200)

Arguments

CPs	output of search_proximalCPs() or adjust_proximalCPs()
output.all	A logical(1), indicating whether to output entries with only single CP site for a 3' UTR.
DIST2END	An integer(1) vector, specifying minimal length difference between proximal and distal APA sites which should be met to be considered for outputted if output.all is set to TRUE. Default is 200 bp.

Value

a data.frame with columns: "fit_value", "Predicted_Proximal_APA", "Predicted_Distal_APA", "utr3start", "utr3end", "Predicted_Distal_APA_type"

Author(s)

Jianhong Ou

See Also

adjust_proximalCPs(), adjust_proximalCPsByPWM(), adjust_proximalCPsByNBC(), get_PAscore2()

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.