1 1 new file mode 100644 ... ... @@ -0,0 +1,58 @@ 1 +\name{writeSimContFastq} 2 +% 3 +\alias{writeSimContFastq} 4 +% 5 +\title{writeSimContFastq: Create FASTQ files with simulated k-mer sequences} 6 +% 7 +\description{Writes compressed FASTQ files where sequence sections contain 8 + concatenated k-mers which are uniformly distributed in the range of k-mers 9 + for given k. 10 + A fraction of the reads can be contaminated with one or more deterministic 11 + k-mers.} 12 +% 13 +\usage{ writeSimContFastq(k=6, nk=5, nSeq=10, pos=1, 14 + kIndex=1, nContam=nSeq, filename="simc.fq.gz")} 15 +% 16 +\arguments{ 17 + \item{k}{\code{numeric}. Length of k-mer. Default value is 6.} 18 + % 19 + \item{nk}{\code{numeric}. Number of k-mers in each FASTQ read. Default 20 + value is 5.} 21 + % 22 + \item{nSeq}{\code{numeric}. Number of simulated reads in FASTQ-file.  23 + Default value is 10.} 24 + % 25 + \item{pos}{\code{numeric}. Determines at which position in sequence the  26 + k-mer is inserted. 1-based (1=first position).} 27 + % 28 + \item{kIndex}{\code{numeric}. k-mer index of inserted k-mer. 29 + The k-mer index can be retreaved for a given k-mer with 'kMerIndex'.} 30 + % 31 + \item{nContam}{\code{numeric}. Absolute number of contaminated reads. 32 + The k-mer's are inserted at the firsts 'nContam' reads 33 + of the sequence array.} 34 + % 35 + \item{filename}{\code{character}. Name of written (compressed) FASTQ file.} 36 +} 37 +\details{The read headers are consequtive numbered. The phred quality values  38 + are equally set to 46 (='.') which represents a phred value of 13. This 39 + function is not designed for routine use. The random content FASTQ files 40 + can be used in order to measure the separation capabilities of hierarchical 41 + clustering mechanisms.} 42 +% 43 +\value{None.} 44 +% 45 +\references{ 46 +Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM 47 +The sanger FASTQ file format for sequences with quality scores and 48 + the Solexa/Illumina FASTQ variants. 49 +Nucleic Acids Research 2010 Vol.38 No.6 1767-1771} 50 +% 51 +\author{Wolfgang Kaisers} 52 +% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - % 53 +% Examples 54 +% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - % 55 +\examples{ 56 +\dontrun{writeSimContFastq()} 57 +} 58 +\keyword{writeSimContFastq}