drawStat {ASEB} | R Documentation |
This function is used to show P-values and enrichment scores for all lysine sites on a specific protein.
drawStat(curveInfoDataFrame, proteinIds=NULL, outputDir=NULL, figKind=c("pdf","jpeg")) ## S4 method for signature 'data.frame' drawStat(curveInfoDataFrame, proteinIds=NULL, outputDir=NULL, figKind=c("pdf","jpeg"))
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. |
outputDir |
character(1), output directory name for all the figures. |
figKind |
character(1), fig format: |
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
.
SequenceInfo
,
readSequence
,
asebSites
,
asebProteins
,
drawEScurve
.
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(),"\n")