ASEB (version 1.16.0)

drawStat: draw P-values and enrichment scores for all lysine sites on a specific protein

Description

This function is used to show P-values and enrichment scores for all lysine sites on a specific protein.

Usage

drawStat(curveInfoDataFrame, proteinIds=NULL, outputDir=NULL, figKind=c("pdf","jpeg"))
## S3 method for class 'data.frame':
drawStat(curveInfoDataFrame, proteinIds=NULL, outputDir=NULL, figKind=c("pdf","jpeg"))

Arguments

curveInfoDataFrame

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

proteinIds

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

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 P-values and enrichment scores for all lysine sites on a specific protein. The X-axis shows positions of all lysine sites on a specific protein, and Y-axis shows the enrichment scores (0~1) and P-values (0~1) for each lysine site. The data.frame object contains curve information is given by asebProteins.

See Also

SequenceInfo, readSequence, asebSites, asebProteins, drawEScurve.

Examples

backgroundSites <- readSequence(system.file("extdata", "background_sites.fa", package="ASEB")) 
    prodefinedSites <- readSequence(system.file("extdata", "predefined_sites.fa", package="ASEB"))
    testProteins <- readSequence(system.file("extdata", "proteins_to_test.fa", package="ASEB"))
    resultList <- asebProteins(backgroundSites, prodefinedSites, testProteins, permutationTimes=100)
    #drawEScurve(resultList$curveInfo, max_p_value=0.5, min_es=0, outputDir=tempdir(), figKind="jpeg")
    drawStat(resultList$curveInfo, outputDir=tempdir(), figKind="jpeg");
    cat("see figures in output dir:", tempdir(),"")