ASEB (version 1.16.0)

drawEScurve: draw Enriment Score curves for specific sites

Description

This function is used to draw Enriment Score curves for specific sites.

Usage

drawEScurve(curveInfoDataFrame, sites=NULL, max_p_value=0.1, min_es=0.2, outputDir=NULL, figKind=c("pdf","jpeg"))
## S3 method for class 'data.frame':
drawEScurve(curveInfoDataFrame, sites=NULL, max_p_value=0.1, min_es=0.2, outputDir=NULL, figKind=c("pdf","jpeg"))

Arguments

curveInfoDataFrame

data.frame object: contains curve information for sites, see example.

sites

character vector: only draw curves for sites with ids appear in this vector. default: draw curves for all the sites appear in curveInfoDataFrame.

max_p_value

numeric(1), only draw curves for sites with p-value less than this value.

min_es

numeric(1), only draw curves for sites with Enriment Score more than this value.

outputDir

character(1), output directory name for all the figures.

figKind

character(1), fig format: "pdf" or "jpeg".

Details

This function is used to draw Enrichment Score curves for specific sites. These curves show running-sum process for calculating enrichment score. The data.frame object contains curve information is given by asebSites or asebProteins.

See Also

SequenceInfo, readSequence, asebSites, asebProteins, drawStat.

Examples

backgroundSites <- readSequence(system.file("extdata", "background_sites.fa", package="ASEB")) 
    prodefinedSites <- readSequence(system.file("extdata", "predefined_sites.fa", package="ASEB"))
    testSites <- readSequence(system.file("extdata", "sites_to_test.fa", package="ASEB"))
    resultList <- asebSites(backgroundSites, prodefinedSites, testSites, permutationTimes=100)
    drawEScurve(resultList$curveInfo, max_p_value=0.1, min_es=0.1, outputDir=tempdir(), figKind="jpeg")
    cat("see figures in output dir:", tempdir(),"")

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