write.listedDNAStringSet: Write a fasta file per sample in parallel

Description Usage Arguments Note See Also Examples

View source: R/hiReadsProcessor.R

Description

Given a listed DNAStringSet object return from extractSeqs, the function writes a fasta file for each sample as defined in filePath parameter.

Usage

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write.listedDNAStringSet(dnaSet, filePath = ".", filePrefix = "processed",
  prependSamplenames = TRUE, format = "fasta", parallel = FALSE)

Arguments

dnaSet

listed DNAStringSet object containing sequences to be written.

filePath

a path write the fasta files per sample. Default is current working directory.

filePrefix

prefix the filenames with a string. Default is 'processed' followed by samplename.

prependSamplenames

Prepend definition lines with samplenames. Default is TRUE. Make sure the dnaSet parameter is a named list where names are used as samplenames.

format

either fasta (the default) or fastq.

parallel

use parallel backend to perform calculation with BiocParallel. Defaults to TRUE. If no parallel backend is registered, then a serial version is ran using SerialParam.

Note

See Also

findBarcodes, read.SeqFolder, extractSeqs, addListNameToReads

Examples

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load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
samples <- c('Roth-MLV3p-CD4TMLVWell6-Tsp509I', 
'Roth-MLV3p-CD4TMLVWell6-MseI', 'Roth-MLV3p-CD4TMLVwell5-MuA')
seqs <- extractSeqs(seqProps, sector='2', samplename=samples, feature="primed")
write.listedDNAStringSet(seqs)

malnirav/hiReadsProcessor documentation built on Sept. 17, 2017, 10:56 a.m.