meltDownK: meltDownK: Condensing DNA k-mer count data to lower k-value...

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

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 <= old k.

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.

Value

S4 Object of class 'Fastqq'.

Note

The meltDownK mechanism is assotiated with a change of DNA k-mer count values (by its accumulative character). Also, count values from down-melted tables are not identical to directly counted values for lower k. For example counting 'AAAA' with k=1 yields four 'A'. Counting 'AAAA' with k=2 yields three 'AA'. As meltDownK sums up count values by prefix k-mers, the melted count table for the second (k=2) count will return three 'A'. Another source for differences may be N-nucleotides. Counting 'AANA' returns three 'A' (using k=1) but only one 'AA' for k=2.

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

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)

wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.