InPAS (version 1.4.4)

proximalAdjByCleanUpdTSeq: adjust the proximal CP sites by cleanUpdTseq

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)

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

Value

the offset of positions of CP sites after filter

Details

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

See Also

proximalAdjByPWM, proximalAdj, PAscore2