Rqc (version 1.6.2)

stats4trim: 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.

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)