Usage of writeFastq function from ShortRead

[zisis86]

Hi,
I am totaly new and i have a question about the syntax of writeFastq function.
I have this script that search for primer sequences in a file and saves good reads from fuzzy in .good.fq file and bad reads in .bad.fq file> i want to use writeFastq functions from ShortRead package to save "good" reads from fuzzy match in "*.good.fq" file and "bad" reads in *".bad.fq" file.Can you help me with the code that i have to fill in in order to do this .
here is my code until now.

gc()
rm(list=ls())
library(ShortRead)
#library(Biostrings)

#read bait sequences
baitseq <- readLines("/home/users/bait_seq.txt")
baitseq

#choose case
num <- 1
exptPath <- "/home/users/INDEX1.fastq"
exptPath

#read data
fq <- readFastq(dirPath=exptPath)
sread(fq)

#count ocurrences of bait
pos <- grepl(baitseq[num],sread(fq))
pos[1:25]
# number of reads
length(pos)
# number of hits
sum(pos)

# fuzzy match - 2 substitutions
fpos <- agrep(baitseq[num],sread(fq), max = list(sub = 2, ins=0, del=0))
fpos[1:25]
# number of fuzzy hits
length(fpos)

# writeFastq functions in ShortRead package to save "good" reads from fuzzy match in "*.good.fq" file and "bad" reads in *".bad.fq" file # ???????
............


#tables
#table <- tables(sread(fq), n=5)
#table$top