Description Usage Arguments Details Value Methods (by class) Author(s) See Also Examples
Process a set of files and returns a list of quality control data. Files must be FASTQ format, compressed or not.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | rqcQA(x, sample = TRUE, n = 1e+06, group = rep("None", length(x)),
top = 10, pair = seq_along(x), ...)
## S4 method for signature 'list'
rqcQA(x, sample, n, group, top, pair,
workers = multicoreWorkers())
## S4 method for signature 'character'
rqcQA(x, sample = TRUE, n = 1e+06,
group = rep("None", length(x)), top = 10, pair = seq_along(x),
workers = multicoreWorkers())
## S4 method for signature 'BamFile'
rqcQA(x, sample, n, group, top, pair)
## S4 method for signature 'FastqFile'
rqcQA(x, sample, n, group, top, pair)
|
x |
input file(s) |
sample |
It reads a random sample from files if this parameter is TRUE. |
n |
Number of sequences to read from each input file. This represents sample size if 'sample' parameter is TRUE, if not represents the chunk size to read on each iteration. Default is read a sample of one million sequences from each input file. |
group |
group name for each input file. |
top |
number of top over-represented reads. Default is 10 reads. |
pair |
combination of files for paired-end reads. By default, all input
files are treated as single-end. For paired-end, please define a vector of
numbers where two index with the same value represent a pair. Examples,
single-end |
... |
other parameters |
workers |
number of parallel workers |
Input files are read using FastStreamer
and FastSampler
classes of ShortRead
package. Process multiple files in
parallel using bplapply
function of BiocParallel
package.
A named list of RqcResultSet
objects, each one represents a
file.
list
: process a list of FastqFile
and
BamFile
objects.
character
: automatically detects file format
(using detectFileFormat
function) of input files then process.
BamFile
: process only one BAM file.
FastqFile
: process only one FASTQ file.
Welliton Souza
1 2 3 4 5 6 | 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")
rqcReadQualityPlot(rqcResultSet)
|
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