parameters-class: Class "parameters"
In CharlesJB/mpiGadem: de novo motif discovery

Description Objects from the Class Slots Author(s) See Also Examples

This object contains contains parameters of GADEM analysis

Objects can be created by calls of the form new("motif_gadem", ...).

numWordGroup: :Number of non-zero k-mer groups.
numTop3mer: :Number of top-ranked trimers for spaced dyads (default: 20).
verbose: :Print immediate results on screen [1-yes (default), 0-no].
numTop4mer: :Number of top-ranked tetramers for spaced dyads (default: 40).
numTop5mer: :Number of top-ranked pentamers for spaced dyads (default: 60).
numGeneration: :Number of genetic algorithm (GA) generations (default: 5).
populationSize: :GA population size (default: 100).
pValue: :P-value cutoff for declaring BINDING SITES (default: 0.0002).
eValue: :ln(E-value) cutoff for selecting MOTIFS (default: 0.0).
extTrim: :Base extension and trimming (1 -yes, 0 -no) (default: 1).
minSpaceWidth: :Minimal number of unspecified nucleotides in spaced dyads (default: 0).
maxSpaceWidth: :Maximal number of unspecified nucleotides in spaced dyads (default: 10).
useChIPscore: :Use top-scoring sequences for deriving PWMs.
numEM: :Number of EM steps (default: 40).
fEM: :Fraction of sequences used in EM to obtain PWMs in an unseeded analysis (default: 0.5).
widthWt: :For -posWt 1 or 3, width of central sequence region with large EM weights for PWM optimization (default: 50).
fullScan: :GADEM keeps two copies of the input sequences internally.
slideWinPWM: :Sliding window for comparing pwm similarity (default : 6).
stopCriterion
numBackgSets: :Number of sets of background sequences (default: 10).
weightType: :Weight profile for positions on the sequence.
bFileName: :Reading user-specified background models.
Spwm: :File name for the seed PWM, when a seeded approach is used.
nSequences: :Number of input sequences.
maskR: :Mask low-complexity sequences or repeats.
nmotifs: :Maximal number of motifs sought.