overRep2Fasta {ngsReports} | R Documentation |
Output overrepresented sequences to disk in fasta format.
overRep2Fasta(x, path, n = 10, labels, noAdapters = TRUE, ...) ## S4 method for signature 'ANY' overRep2Fasta(x, path, n = 10, labels, noAdapters = TRUE, ...) ## S4 method for signature 'FastqcData' overRep2Fasta(x, path, n = 10, labels, noAdapters = TRUE, ...) ## S4 method for signature 'FastqcDataList' overRep2Fasta(x, path, n = 10, labels, noAdapters = TRUE, ...)
x |
Can be a |
path |
Path to export the fasta file to. Reverts to a default in the working directory if not supplied |
n |
The number of sequences to output |
labels |
An optional named factor of labels for the file names. All filenames must be present in the names. File extensions are dropped by default. |
noAdapters |
logical. Remove any sequences identified as possible adapters or primers by FastQC |
... |
Used to pass any alternative patterns to remove from the end of filenames |
Fasta will contain Filename
, Possible Source
,
Percent of total reads
Exports to a fasta file, and returns the fasta information invisibly
# Get the files included with the package packageDir <- system.file("extdata", package = "ngsReports") fl <- list.files(packageDir, pattern = "fastqc.zip", full.names = TRUE) # Load the FASTQC data as a FastqcDataList object fdl <- FastqcDataList(fl) # Export the top10 Overrepresented Sequences as a single fasta file faOut <- file.path(tempdir(), "top10.fa") overRep2Fasta(fdl, path = faOut)