RqcResultSet-class: Class RqcResultSet

In Rqc: Quality Control Tool for High-Throughput Sequencing Data

Description

Class RqcResultSet

Frequency distribution of cycle-specific base call

Frequency distribution of cycle-specific quality

File information

Top over-represented sequencing reads

Read frequency table

Frequency distribution of per read mean quality

Frequency distribution of read width

Usage

perCycleBasecall(x)

## S4 method for signature 'RqcResultSet'
perCycleBasecall(x)

## S4 method for signature 'list'
perCycleBasecall(x)

perCycleQuality(x)

## S4 method for signature 'RqcResultSet'
perCycleQuality(x)

## S4 method for signature 'list'
perCycleQuality(x)

perFileInformation(x)

## S4 method for signature 'RqcResultSet'
perFileInformation(x)

## S4 method for signature 'list'
perFileInformation(x)

perFileTopReads(x)

## S4 method for signature 'RqcResultSet'
perFileTopReads(x)

## S4 method for signature 'list'
perFileTopReads(x)

perReadFrequency(x)

## S4 method for signature 'RqcResultSet'
perReadFrequency(x)

## S4 method for signature 'list'
perReadFrequency(x)

perReadQuality(x)

## S4 method for signature 'RqcResultSet'
perReadQuality(x)

## S4 method for signature 'list'
perReadQuality(x)

perReadWidth(x)

## S4 method for signature 'RqcResultSet'
perReadWidth(x)

## S4 method for signature 'list'
perReadWidth(x)

Arguments

x	RqcResultSet object or list of RqcResultSet objects

Value

data frame

data frame

data frame

data frame

data frame

data frame

data frame

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")
head(perCycleBasecall(rqcResultSet))
head(perCycleQuality(rqcResultSet))
head(perReadFrequency(rqcResultSet))
head(perReadQuality(rqcResultSet))
head(perReadWidth(rqcResultSet))
perFileInformation(rqcResultSet)
perFileTopReads(rqcResultSet)

Rqc documentation built on Nov. 8, 2020, 5:11 p.m.