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

the position weight matrix(PWM) motif database object, which contains the motif model of each transcription factor family. [as PWMDatabase]

search.regions

the sequence regions for run the motif site scan, which can be a fasta sequence collection, a FastaFile object or a character vector of the raw sequence data, each sequence is a candidate promoter/upstream sequence region of one gene.

family

an optional character vector of the transcription factor family name for restrict the motif scan: only the motif model of the given families will be used for the scan, all of the motif models in the database will be used if this parameter is not specified.

pval.cutoff

the p-value cutoff of the motif site match: the candidate site that its match p-value is greater than this cutoff will be ignored, by default is 0.05. [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 parameter only. [as double]

top

the top n best matched site of each motif model on each sequence region, by default is 3. [as integer]

bg

the background model of the motif site scan, the uniform background model will be used if this parameter is not specified. [as BackgroundModel]

scan.reverse

scan the motif site on the reverse complement strand of the sequence region or not? by default is TRUE. [as boolean]

tqdm.bar

display the progress bar of the motif site scan task on the console? by default is TRUE. [as boolean]

env

the R# runtime environment object. [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]