44 lines
1.2 KiB
R
Executable File
44 lines
1.2 KiB
R
Executable File
titvFPEst <- function(titvExpected, titvObserved) { 1 - (titvObserved - 0.5) / (titvExpected - 0.5) }
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calcHet <- function(nknown, knownTiTv, nnovel, novelTiTv, callable) {
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TP <- nknown + (1-titvFPEst(knownTiTv, novelTiTv)) * nnovel
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2 * TP / 3 / callable
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}
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marginalTiTv <- function( nx, titvx, ny, titvy ) {
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tvx = nx / (titvx + 1)
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tix = nx - tvx
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tvy = ny / (titvy + 1)
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tiy = ny - tvy
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tiz = tix - tiy
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tvz = tvx - tvy
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return(tiz / tvz)
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}
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marginaldbSNPRate <- function( nx, dbx, ny, dby ) {
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knownx = nx * dbx / 100
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novelx = nx - knownx
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knowny = ny * dby / 100
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novely = ny - knowny
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knownz = knownx - knowny
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novelz = novelx - novely
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return(knownz / ( knownz + novelz ) * 100)
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}
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numExpectedCalls <- function(L, theta, calledFractionOfRegion, nIndividuals, dbSNPRate) {
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nCalls <- L * theta * calledFractionOfRegion * sum(1 / seq(1, 2 * nIndividuals))
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return(list(nCalls = nCalls, nKnown = dbSNPRate * nCalls, nNovel = (1-dbSNPRate) * nCalls))
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}
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normalize <- function(x) {
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x / sum(x)
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}
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normcumsum <- function(x) {
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cumsum(normalize(x))
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}
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cumhist <- function(d) {
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h <- hist(d)
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#plot(h$mids, cumsum(h$count), type="b", col="orange", lwd=2)
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}
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