gcContentMatrix: gcContentMatrix: Returns matrix with read counts for GC...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

Description Usage Arguments Details Value Author(s) References See Also Examples

Returns a matrix with read counts.

1	gcContentMatrix(object)

object

Fastqq: Object from wich data is copied.

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).

matrix.

Wolfgang Kaisers

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

gcContent

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)