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use inclusive cutoffs for aberrant event detection (#37)
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Co-authored-by: Christian Mertes <[email protected]>
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nickhsmith and c-mertes authored Apr 7, 2022
1 parent 45764d9 commit 6e2ce01
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Showing 3 changed files with 7 additions and 7 deletions.
4 changes: 2 additions & 2 deletions NEWS
Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,10 @@ CHANGES IN VERSION 1.6.1
o Require min expression in 5% instead of 95% of the samples
o Require min expression on both sides of the junction
o Align FRASER package with DROP pipeline (#24)
o Move temp directory from tempdir() to working directory getwd()
o Move temp directory from tempdir() to working directory getwd() (#35)
o Improve visualizations and Improve documentation
o Improve internal object validation
o Minor bugfixes
o Minor bugfixes (eg. #37)

CHANGES IN VERSION 1.2.1
o Add merging of external counts
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6 changes: 3 additions & 3 deletions R/AllGenerics.R
Original file line number Diff line number Diff line change
Expand Up @@ -920,13 +920,13 @@ aberrant.FRASER <- function(object, type=currentType(object), padjCutoff=0.05,
goodCutoff <- goodCutoff & as.matrix(n >= minCount)
}
if(!is.na(zScoreCutoff)){
goodCutoff <- goodCutoff & as.matrix(abs(zscores) > zScoreCutoff)
goodCutoff <- goodCutoff & as.matrix(abs(zscores) >= zScoreCutoff)
}
if(!is.na(deltaPsiCutoff)){
goodCutoff <- goodCutoff & as.matrix(abs(dpsi) > deltaPsiCutoff)
goodCutoff <- goodCutoff & as.matrix(abs(dpsi) >= deltaPsiCutoff)
}
if(!is.na(padjCutoff)){
goodCutoff <- goodCutoff & as.matrix(padj < padjCutoff)
goodCutoff <- goodCutoff & as.matrix(padj <= padjCutoff)
}
goodCutoff[is.na(goodCutoff)] <- FALSE

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4 changes: 2 additions & 2 deletions R/plotMethods.R
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Expand Up @@ -213,8 +213,8 @@ plotVolcano.FRASER <- function(object, sampleID,
}

if(!is.na(padjCutoff)){
if(dt[,any(padj < padjCutoff)]){
padj_line <- min(dt[padj < padjCutoff, -log10(pval)])
if(dt[,any(padj <= padjCutoff)]){
padj_line <- min(dt[padj <= padjCutoff, -log10(pval)])
}
if(!"padj_line" %in% ls() || padj_line > 10 || is.na(padj_line)){
padj_line <- 6
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