parameters-class {rGADEM}R Documentation

Class "parameters"

Description

This object contains contains parameters of GADEM analysis

Objects from the Class

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

Slots

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.

Author(s)

Arnaud Droit arnaud.droit@crchuq.ulaval.ca

See Also

gadem , align, motif

Examples

showClass("parameters")

[Package rGADEM version 2.42.0 Index]