runFastQC-methods: A wrapper for the bash shell command fastqc.

In ngsReports: Load FastqQC reports and other NGS related files

Description

\lifecycle

soft-deprecated A convenient wrapper for the bash shell command fastqc. Only runs if Fastqc is installed.

Usage

runFastQC(
  object,
  outPath,
  threads = 1L,
  casava = FALSE,
  nofilter = FALSE,
  extract = FALSE,
  nogroup = FALSE,
  min_length = 1,
  contaminants = c(),
  adapters = c(),
  kmers = 7,
  exec
)

## S4 method for signature 'ANY'
runFastQC(
  object,
  outPath,
  threads = 1L,
  casava = FALSE,
  nofilter = FALSE,
  extract = FALSE,
  nogroup = FALSE,
  min_length = 1,
  contaminants = c(),
  adapters = c(),
  kmers = 7,
  exec
)

## S4 method for signature 'FastqFile'
runFastQC(
  object,
  outPath,
  threads = 1L,
  casava = FALSE,
  nofilter = FALSE,
  extract = FALSE,
  nogroup = FALSE,
  min_length = 1,
  contaminants = c(),
  adapters = c(),
  kmers = 7,
  exec
)

## S4 method for signature 'FastqFileList'
runFastQC(
  object,
  outPath,
  threads = 1L,
  casava = FALSE,
  nofilter = FALSE,
  extract = FALSE,
  nogroup = FALSE,
  min_length = 1,
  contaminants = c(),
  adapters = c(),
  kmers = 7,
  exec
)

## S4 method for signature 'BamFile'
runFastQC(
  object,
  outPath,
  threads = 1L,
  casava = FALSE,
  nofilter = FALSE,
  extract = FALSE,
  nogroup = FALSE,
  min_length = 1,
  contaminants = c(),
  adapters = c(),
  kmers = 7,
  exec
)

## S4 method for signature 'BamFileList'
runFastQC(
  object,
  outPath,
  threads = 1L,
  casava = FALSE,
  nofilter = FALSE,
  extract = FALSE,
  nogroup = FALSE,
  min_length = 1,
  contaminants = c(),
  adapters = c(),
  kmers = 7,
  exec
)

Arguments

object	A FastqFileList, BamFileList, FastqFile, BamFile or character vector of file paths with all objects coercible to a single one of these types.
outPath	The path to write the FastQC reports. Must exist as (for safety) it will not be created when calling this function
threads	The number of threads to run in parallel
casava	logical. Sets the --casava flag
nofilter	logical. Sets the --nofilter flag
extract	logical. Extract the zip files on completion of the report
nogroup	logical. Sets the grouping of bases for reads longer than 50bp
min_length	integer. Sets an artificial lower limit on the length of the sequence to be shown in the report.
contaminants	Path to an alternate file with contaminants. The structure of the file will not be checked. Refer to the fastqc help page for more details
adapters	Path to a file listing adapters to search for. The structure of the file will not be checked. Refer to the fastqc help page for more details
kmers	An integer between 2 and 10
exec	The location of the fastqc executable.

Details

This is a simple wrapper function for controlling & running fastqc from within R. This can be very useful for controlling & documenting an entire pipeline from within knitr to produce a simple report

Takes a FastqFile, FastqFileList, BamFile or BamFileList. Alternatively paths to files which are coerecible to these objects can be passed.

Only the common functionality of FastQC is implemented, for more fine detail please call FastQC directly.

Value

An list of paths to the output

Author(s)

Stephen Pederson <[e-mail]>

Examples

## Not run: 
library(ShortRead)
sp <- SolexaPath(system.file('extdata', package='ShortRead'))
fl <- file.path(analysisPath(sp), "s_1_sequence.txt")
f <- FastqFile(fl)
# This requires a working installation of FastQC
fqcFile <- runFastQC(f, outPath = tempdir())

## End(Not run)

ngsReports documentation built on Nov. 23, 2020, 2:01 a.m.