read_fastq {debar}

Read in raw data from a fastq file.

Description

Read in raw data from a fastq file.

Usage

read_fastq(x, keep_quality = TRUE)

Arguments

x

The name of the fastq file to read data from.

keep_quality

Boolean indicating if the Phred quality scores should be retained in the output dataframe. Default is TRUE.

Examples

#read in an unzipped fastq file
fastq_example_file = system.file('extdata/coi_sequel_data_subset.fastq', 
                                  package = 'debar')
data = read_fastq(fastq_example_file)
#read in a gzipped fastq file and do not keep the phred scores
gz_fastq_example_file = system.file('extdata/coi_sequel_data_subset.fastq', 
                                    package = 'debar')
data2 = read_fastq(gz_fastq_example_file, keep_quality = FALSE)