hiReadsProcessor (version 1.8.2)

read.seqsFromSector: Read fasta/fastq/sff given the path or sampleInfo object.

Description

Given a sequence reads file path, the function returns a DNAStringSet object.

Usage

read.seqsFromSector(seqFilePath = NULL, sector = 1, isPaired = FALSE)

Arguments

seqFilePath

a path to fasta/fastq/sff reads file or a sampleInfo object returned by read.SeqFolder

sector

specific sector to reads sequences from. Default is 1, and not required if seqFilePath is a direct file path rather than sampleInfo object.

isPaired

does the sector contain paired end reads? Default is FALSE

Value

• if isPaired is FALSE, then a DNAStringSet object, else a list of DNAStringSet objects of three elements corresponding to reads from "barcode", "pair1", and "pair2". Note: "pair2" is reverse complemented!

See Also

findBarcodes, read.SeqFolder, extractSeqs

Examples

load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
read.seqsFromSector(seqProps, sector="2")