buildBackgroundModel: build background model

In alyst/dagLogo: dagLogo

Description

build background model for dag test

Usage

buildBackgroundModel(dagPeptides, 
                                 bg=c("wholeGenome", "inputSet", "nonInputSet"),
                                 model=c("any", "anchored"),
                                 targetPosition=c("any", "Nterminus", "Cterminus"),
                                 uniqueSeq=TRUE,
                                 permutationSize=30L,
                                 rand.seed=1,
                                 replacement=FALSE,
                                 proteome)

Arguments

dagPeptides	an object of dagPeptides, output of fetchSequence or formatSequence
bg	could be "wholeGenome", "inputSet" or "nonInputSet"
model	could be "any" or "anchored"
targetPosition	could be "any", "Nterminus" or "Cterminus"
uniqueSeq	should the background sequence be unique?
permutationSize	how many times should it samples
rand.seed	random seed
replacement	Should sampling be with replacement?
proteome	an object of Proteome, output of prepareProteome

Details

The background could be generated from wholeGenome, inputSet or nonInputSet. whole genome: randomly select subsequences from the whole genome with each subsequence containing amino acids with same width of input sequences. anchored whole genome: randomly select subsequences from the whole genome with each subsequence containing amino acids with same width of input sequences where the middle amino acids must contain anchor amino acid, e.g., K, which is specified by user. input set: same to whole genome, but only use protein sequence from input id and not including the site specified in input sequences anchored input set: same to anchored whole genome, but only use protein sequences from input id, and not including the site specified in input sequences. non-input set: whole genome - input set. anchored non-input set: whole genome - input set and the middle amino acids must contain anchor amino acid.

Value

an object of dagBackground which contains background and permutationSize.

Author(s)

Jianhong Ou, Alexey Stukalov, Julie Zhu

See Also

prepareProteome

Examples

    data("seq.example")
    data("proteome.example")
    bg <- buildBackgroundModel(seq.example, proteome=proteome.example)

alyst/dagLogo documentation built on May 12, 2019, 2:32 a.m.