proximalAdjByCleanUpdTSeq {InPAS} | R Documentation

## 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, 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`

[Package InPAS version 1.14.2 Index]