stats4trim: Minimun read mean quality and maximum percentage loss of...
In Rqc: Quality Control Tool for High-Throughput Sequencing Data

Description Usage Arguments Value Author(s) Examples

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.

1	stats4trim(rqcResultSet, qmin, pmax)

`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.

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

Welliton Souza

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)