rseq {cosmo} | R Documentation |
Random generation of DNA sequence according to ZOOPS or TCM model
Description
This function randomly generates a number of DNA sequences that
contain a given motif accordint to the ZOOPS or TCM model. In the
ZOOPS model, each sequence contains one or zero occurrences of the
motif. In the TCM model, each sequence may contain an arbitrary number
of motif occurrences.
Usage
rseq(numSeqs, seqLength, rate, pwm, transMats,
model="ZOOPS", posOnly=FALSE)
Arguments
numSeqs |
numeric The number of sequences to be generated |
seqLength |
numeric The length of each sequence. This may
be either a single number, in which case that number is taken to be
the common length of all sequence, or a vector of sequence lengths. |
rate |
numeric In the ZOOPS model, this is the proportion
of sequences containg a motif occurrence. In the TCM model, this the
rate parameter lambda with which motifs are inserted into the sequences. |
pwm |
numeric Position-weight matrix of the motif to be inserted. |
transMats |
The transition matrices to use for the
background Markov model. This is a list of matrices, with the first
matrix given the transition probabilities for the 0th order Markov
model, the second matrix giving the transition probabilities for a
1st order Markov model, and so on. |
model |
Either "ZOOPS" or "TCM" |
posOnly |
logical If TRUE, motifs are inserted only in the
forwards orientation. Otherwise, motifs are inserted in either of
the two possible orientations with equal probabilities. |
Value
seqs |
A list with one element for each sequence in the file. The
elements are in two parts, one the description and the second a
character string of the biological sequence. |
motifs |
An "align" object summarizing the positions of the
inserted motif occurrences. |
empPWM |
An object of class pwm representing the position
weight matrix obtained by aligning the inserted motifs. |
Author(s)
Oliver Bembom, bembom@berkeley.edu
Examples
## generate 20 sequences according to ZOOPS model
## with an expected number of 10 sequences containing a
## motif
data(motifPWM)
data(transMats)
res <- rseq(20, 250, 0.5, motifPWM, transMats,"ZOOPS")
[Package
cosmo version 1.8.0
Index]