knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(fastqR)

This is a short document to demonstrate the usage of the fastqR package. The main functions of the package are laid out below:

Parsing FastQ files

You can parse a fastq file as shown below:

read_fastq(system.file("good.fq", package = "fastqR")) -> fastq_data
fastq_data

You can also manually do a calculation of GC content

gc_content(c("GATCGCGATGCTATGCGTATGCG","TAGTATTGCTATTATATGATTA"))

Decoding of encoded Phred scores

The quality scores in a fastq file are encoded Phred scores. We have a function which can decode them.

decode_qualities(fastq_data$Qualities[1])


rafalkol/fastqR documentation built on Dec. 22, 2021, 12:01 p.m.