filter results
estimate the cpsites
calculate SSE
predict the cleavage and polyadenylation(CP) site
do fisher exact test for two group datasets
alternative polyadenylation and cleavage estimations
do estimation of alternative polyadenylation and cleavage site in one step
do analysis for single group samples
do analysis for single sample
sort GRanges
do test for dPDUI
get the local minimal square standard error (SSE)
calculate local background cutoff value
calculate the CP score
get sequence lengths
search proximal CPsites
prepare coverage data and fitting data for plot
3'UTR annotation for hg19 obtained from utr3Annotation
calculate the depth weight for each example
adjust distal CP sites by cleanUpdTSeq
proximalAdjByCleanUpdTSeq
adjust the proximal CP sites by cleanUpdTseq
adjust the proximal CP sites by PWM
trim the sequence names
total coverage
extract coverage of last CDS exon region
use limma to analyze the PDUI
3'UTR annotation for mm10 obtained from utr3Annotation
prepare the files for GSEA analysis
extract 3'UTR from TxDb object
adjust the proximal CP sites
claculate coverage for giving region
extract coverage from bedgraph file
prepare dataset for test
remove the candicates LIKE UTR3___UTR3
extract long and short 3UTR region
search distal CP sites
Class UTR3eSet
extract coverage of 3UTR for CP sites prediction
read coverage from bedGraph files
calculate the cutoff threshold of coverage
calculate the CP score
polish the searching results of CP sites
calculate the usage of long and short form of UTR3
estimation of 3'UTR usage for each region