seqTools (version 1.6.0)

meltDownK: meltDownK: Condensing DNA k-mer count data to lower k-value (i.e. shorter DNA motifs).

Description

Returns a copy of given object where DNA k-mer counts and first DNA k-mer count table are reduced in size.

Usage

meltDownK(object, newK)

Arguments

object

Fastqq: Object from wich data is copied.

newK

integer: New value for k. Must be >=1 and

Value

Details

The function sums all count values which belong the the new motif up. The new motif is the new-k sized prefix of the given k-mer motif.

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

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 <- meltDownK(fq, 2)