filterFeatures {SGSeq} | R Documentation

## Filter predicted features

### Description

Filter previously predicted features using more stringent criteria.

### Usage

    filterFeatures(features, paired_end, read_length, frag_length, lib_size,
      min_junction_count = NULL, alpha, psi, beta, gamma)

### Arguments

`features` | `TxFeatures` object with predicted features, including metadata columns “N”, “N_splicesite” and “coverage”.
`paired_end` | Logical, `TRUE` for paired-end data, `FALSE` for single-end data
`read_length` | Read length required for use with `alpha`
`frag_length` | Fragment length for paired-end data required for use with `alpha`
`lib_size` | Number of aligned fragments required for use with `alpha`
`min_junction_count` | Minimum fragment count required for a splice junction to be included. If specified, argument `alpha` is ignored.
`alpha` | Minimum FPKM required for a splice junction to be included. Internally, FPKMs are converted to counts, requiring arguments `read_length`, `frag_length` and `lib_size`. `alpha` is ignored if argument `min_junction_count` is specified.
`psi` | Minimum splice frequency required for a splice junction to be included
`beta` | Minimum relative coverage required for an internal exon to be included
`gamma` | Minimum relative coverage required for a terminal exon to be included

### Details

Initial predictions with `predictTxFeatures` must have been performed with `include_counts = TRUE` and `retain_coverage = TRUE`, so that predicted features contain metadata columns “N”, “N_splicesite” and “coverage”.

### Value

`TxFeatures` object with filtered features

### Author(s)

Leonard Goldstein

[Package SGSeq version 1.16.2 Index]