motif_search {TRN.builder} R Documentation

scan the TF binding site motif on the given sequence regions

Description

Usage

motif_search(db, search.regions,
    family = NULL,
    pval.cutoff = 0.05,
    minW = 0.85,
    top = 3,
    bg = NULL,
    scan.reverse = TRUE,
    tqdm.bar = TRUE);

Arguments

db

[as PWMDatabase]

search.regions

the sequence regions for run the motif site scan, which can be a fasta sequence collection, a @T:SMRUCC.genomics.SequenceModel.FASTA.FastaFile

family

pval.cutoff

[as double]

minW

the minimum score ratio cutoff of the motif site match, by default is 0.85.

NOTE: this parameter is not applied by the current implementation, the motif site match result is filtered by the pval_cutoff and the top. [as double]

top

[as integer]

bg

[as BackgroundModel]

scan.reverse

[as boolean]

tqdm.bar

[as boolean]

env

[as Environment]

Details

Authors

TRNtoolkit

Value

a vector of the MotifMatch motif site match result: the title property is the sequence title of the corresponding sequence region, the motif property is the matched motif model, the start, ends, strand and segment property is the location and the sequence data of the matched site, and the score1, score2 and pvalue property is the match score data;

this function returns a R# error message object if the given sequence source can not be cast to a fasta sequence collection.

clr value class

Examples

[Package TRN.builder version 1.0.0.0 Index]