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

In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

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 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")

hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.