gcContentMatrix {seqTools} | R Documentation |
Returns a matrix with read counts. getGCcontent returns a numeric vector with the GC contend (in percent) for each fastq file.
gcContentMatrix(object)
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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
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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) getGCcontent(fq)