Rqc (version 1.6.2)

RqcResultSet-class: 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)
"perCycleBasecall"(x)
"perCycleBasecall"(x)
perCycleQuality(x)
"perCycleQuality"(x)
"perCycleQuality"(x)
perFileInformation(x)
"perFileInformation"(x)
"perFileInformation"(x)
perFileTopReads(x)
"perFileTopReads"(x)
"perFileTopReads"(x)
perReadFrequency(x)
"perReadFrequency"(x)
"perReadFrequency"(x)
perReadQuality(x)
"perReadQuality"(x)
"perReadQuality"(x)
perReadWidth(x)
"perReadWidth"(x)
"perReadWidth"(x)

Arguments

x

RqcResultSet object or list of RqcResultSet objects

Value

data framedata framedata framedata framedata framedata framedata 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)