microseq (version 1.0)

readFastq: Read FASTQ files

Description

Reads biological sequences (DNA) in the FASTQ format.

Usage

readFastq(in.file)

Arguments

in.file

url/directory/name of FASTQ file to read.

Value

readFastq returns a Fasta object with the header and sequence part of the FASTQ file.

Details

The FASTQ format is typically used for storing DNA sequences (reads) together with quality scores from a sequencer. Reading a FASTQ-file with this function will result in ignoring the quality score string, and the sequences are stored in a Fasta object.

This function uses the readBStringSet function of the Biostrings package.

See Also

readFasta, plot.Fasta, summary.Fasta.

Examples

## Not run: 
# ex.file <- file.path(file.path(path.package("microseq"),"extdata"),"small.fastq")
# fdta <- readFastq(ex.file)
# summary(fdta)
# ## End(Not run)