stats4trim {Rqc} | R Documentation

## Minimun read mean quality and maximum percentage loss of reads estimations for trimming step.

### Description

This function estimates how many reads would be lost if the sequences are filtered by a minimum read mean quality value. Also this function estimates what is the minimum read mean quality value for filtering and lose max percentage defined.

### Usage

    stats4trim(rqcResultSet, qmin, pmax)

### Arguments

`rqcResultSet` | list of `RqcResultSet` objects created by `rqc` and `rqcQA` functions.
`qmin` | Minimum read mean quality value (bewteen 0 and 41).
`pmax` | Maximum percentage of reads permitted been lost during trimming step.

### Value

A data frame containg estimated minimum quality and maximum percentage for each input file.

### Author(s)

Welliton Souza

### Examples

    checkpoint("Rqc", path=system.file(package="Rqc", "extdata"), {
      folder <- system.file(package="ShortRead", "extdata/E-MTAB-1147")
      files <- list.files(full.names=TRUE, path=folder)
      rqcResultSet <- rqcQA(files, pair=c(1,1), workers=1)
    }, keep="rqcResultSet")
    stats4trim(rqcResultSet, qmin=20)
    stats4trim(rqcResultSet, pmax=10)

[Package Rqc version 1.20.0 Index]