search_distalCPs {InPAS} | R Documentation

## search distal CP sites

### Description

search distal CP sites

### Usage

    search_distalCPs(
      chr.cov.merge,
      conn_next_utr3,
      curr_UTR,
      window_size,
      depth.weight,
      long_coverage_threshold,
      background,
      z2s
    )

### Arguments

`chr.cov.merge` | merged coverage data for a given chromosome
`conn_next_utr3` | A logical(1) vector, indicating whether joint to next 3UTR or not (used by `remove_convergentUTR3s()`)
`curr_UTR` | GRanges of 3' UTR for a given chromosome
`window_size` | An integer(1) vector, the window size for novel distal or proximal CP site searching. default: 100.
`depth.weight` | A named vector. One element of an output of `setup_CPsSearch()` for coverage depth weight, which is the output of `get_depthWeight()`
`long_coverage_threshold` | An integer(1) vector, specifying the cutoff threshold of coverage for the terminal of long form 3' UTRs. If the coverage of first 100 nucleotides is lower than coverage_threshold, that transcript will be not considered for further analysis. Default, 2.
`background` | A character(1) vector, the range for calculating cutoff threshold of local background. It can be "same_as_long_coverage_threshold", "1K", "5K","10K", or "50K".
`z2s` | one element of an output of `setup_CPsSearch()` for Z-score cutoff values, which is the output of `get_zScoreCutoff()`

### Value

a list

### Author(s)

Jianhong Ou

### See Also

`get_PAscore2()`

[Package InPAS version 2.2.0 Index]