mergeFastqq: mergeFastqq: Merges two Fastqq object into one.

In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

Description

The contents of two given Fastqq objects are merged together into one resulting Fastqq object.

Usage

mergeFastqq(lhs,rhs)

Arguments

lhs	Fastqq.
rhs	Fastqq.

Details

The data on all FASTQ files in the two incoming objects is merged together. The object has the same internal structure as if the data from all FASTQ files had been collected by a separate call of fastqq on the merged FASTQ file names of the arguments. Duplicated probeLabel's are separated by adding of consecutive numbers as suffix to all probeLabel's. When lhs and rhs contain kmer-counts for different k (getK), the function uses the meltDownK mechanism in order to equalize the k values. Therefore it is possible to compare samples which were counted with different k (i.e. k-mer resolution).

Value

S4 Object of class 'Fastqq'.

Note

Note that the meltDownK mechanism is assotiated with a change of DNA k-mer count values. See 'meltDownK' help (note) for more information.

Author(s)

Wolfgang Kaisers

Examples

basedir<-system.file("extdata",package="seqTools")
setwd(basedir)
#
lhs<-fastqq("g4_l101_n100.fq.gz",k=4,"g4")
rhs<-fastqq("g5_l101_n100.fq.gz",k=4,"g5")
fq<-mergeFastqq(lhs,rhs)

Example output

Loading required package: zlibbioc
[fastqq] File ( 1/1) 'g4_l101_n100.fq.gz'	done.
[fastqq] File ( 1/1) 'g5_l101_n100.fq.gz'	done.

seqTools documentation built on Nov. 8, 2020, 5:20 p.m.