RqcResultSet-class {Rqc} | R Documentation

## Class RqcResultSet

### 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)

[Package Rqc version 1.16.2 Index]