discardLowCoveragePSIvalues {psichomics} | R Documentation

## Remove alternative splicing quantification values based on coverage

### Description

Remove alternative splicing quantification values based on coverage

### Usage

    discardLowCoveragePSIvalues(
      psi,
      minReads = 10,
      vasttoolsScoresToDiscard = c("VLOW", "N")
    )

### Arguments

`psi` | Data frame or matrix: alternative splicing quantification
`minReads` | Currently this argument does nothing
`vasttoolsScoresToDiscard` | Character: if you are using inclusion levels from VAST-TOOLS, filter the data based on quality scores for read coverage, e.g. use `vasttoolsScoresToDiscard = c("SOK", "OK", "LOW")` to only keep events with good read coverage (by default, events are not filtered based on quality scores); read https://github.com/vastgroup/vast-tools for more information on VAST-TOOLS quality scores

### Value

Alternative splicing quantification data with missing values for any values with insufficient coverage

[Package psichomics version 1.20.2 Index]