data(tamoxifen_analysis)
#Retrieve DB sites with FDR < 0.05
tamoxifen.DB <- dba.report(tamoxifen)
tamoxifen.DB
#Retrieve DB sites with p-value < 0.05 and Fold > 2
tamoxifen.DB <- dba.report(tamoxifen, th=.05, bUsePval=TRUE, fold=2)
tamoxifen.DB
#Retrieve all sites with confidence stats
# and how many times each site was identified as a peak
tamoxifen.DB <- dba.report(tamoxifen, th=1, bCalled=TRUE)
tamoxifen.DB
#Retrieve all sites with confidence stats and normalized counts
tamoxifen.DB <- dba.report(tamoxifen, th=1, bCounts=TRUE)
tamoxifen.DB
#Retrieve all sites with confidence stats and raw counts
tamoxifen.DB <- dba.report(tamoxifen, th=1, bCounts=TRUE,bNormalized=FALSE)
tamoxifen.DB
#Retrieve report as a SummarizedObject
tamoxifen.sset <- dba.report(tamoxifen, DataType=DBA_DATA_SUMMARIZED_EXPERIMENT)
tamoxifen.sset
#Retrieve report-based DBA object
data(tamoxifen_counts)
tamoxifen <- dba.contrast(tamoxifen, categories=DBA_CONDITION, block=tamoxifen$masks$MCF7)
tamoxifen <- dba.analyze(tamoxifen,bCorPlot=FALSE)
tamoxifen.DB <- dba.report(tamoxifen,method=c(DBA_DESEQ2,DBA_DESEQ2_BLOCK),
bDB=TRUE, bGain=TRUE, bLoss=TRUE)
dba.plotVenn(tamoxifen.DB,1:4,label1="Single Factor GAIN",label2="Single Factor LOSS",
label3="Blocking Factor GAIN",label4="Blocking Factor LOSS")
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