gcContentMatrix: gcContentMatrix: Returns matrix with read counts for GC...

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

Description

Returns a matrix with read counts. getGCcontent returns a numeric vector with the GC contend (in percent) for each fastq file.

Usage

gcContentMatrix(object)

Arguments

object

Fastqq: Object from wich data is copied.

Details

The matrix contains one column for each FASTQ file. Rows labeled from 0 to 100 which represents percent (%) GC content. The matrix contains numbers of reads with the respective proportion of GC (Row 2 contains number of reads with 2% GC content).

Value

matrix.

Author(s)

Wolfgang Kaisers

References

Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM The sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2010 Vol.38 No.6 1767-1771

See Also

gcContent

Examples

basedir <- system.file("extdata",package="seqTools")
setwd(basedir)
#
fq <- fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4,
    probeLabel=c("g4","g5"))
fqm<-gcContentMatrix(fq)
getGCcontent(fq)

Example output

Loading required package: zlibbioc
[fastqq] File ( 1/2) 'g4_l101_n100.fq.gz'	done.
[fastqq] File ( 2/2) 'g5_l101_n100.fq.gz'	done.
   g4    g5 
46.67 45.10 

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