build background model

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Description

build background model for dag test

Usage

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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

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