read.fastq: Read fastq file

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Read fastq file

Description

Read fastq file

Usage

read.fastq(fileName, convert = FALSE, baseQual = 33, ...)

Arguments

fileName	name of fastq file
convert	if TRUE convert condensed quals to space separated numeric quals
baseQual	integer to subtract from quality characters to convert into quality space
...	additional arguments to readLines

Value

dataframe with name, seq, qual

Examples

fastq<-c(
  "@SEQ_ID",
  "GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT",
  "+",
  "!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65"
)
read.fastq(textConnection(fastq))

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.