From d483c1112e838440f332efece783b20d980d42af Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Tue, 2 Aug 2016 16:27:11 +1000 Subject: Initial implementation --- DESCRIPTION | 9 +++++++++ LICENSE | 13 +++++++++++++ NAMESPACE | 1 + R/pmt.R | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++ man/pmt-package.Rd | 26 ++++++++++++++++++++++++++ man/pmt.Rd | 33 +++++++++++++++++++++++++++++++++ 6 files changed, 135 insertions(+) create mode 100644 DESCRIPTION create mode 100644 LICENSE create mode 100644 NAMESPACE create mode 100644 R/pmt.R create mode 100644 man/pmt-package.Rd create mode 100644 man/pmt.Rd diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..5da1874 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,9 @@ +Package: pmt +Type: Package +Title: Poission Margin Test for Normalisation Free Significance Analysis of NGS Data +Version: 1.0 +Date: 2016-08-02 +Author: Justin Bedo +Maintainer: Justin Bedo +Description: An implementation of the PMT for calling differental counts of NGS data. +License: ISC diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..c462bea --- /dev/null +++ b/LICENSE @@ -0,0 +1,13 @@ +Copyright © 2016 by Justin Bedő + +Permission to use, copy, modify, and/or distribute this software for any +purpose with or without fee is hereby granted, provided that the above +copyright notice and this permission notice appear in all copies. + +THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES +WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR +ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES +WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN +ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR +IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..d75f824 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1 @@ +exportPattern("^[[:alpha:]]+") diff --git a/R/pmt.R b/R/pmt.R new file mode 100644 index 0000000..090ceca --- /dev/null +++ b/R/pmt.R @@ -0,0 +1,53 @@ +# Copyright © 2016 by Justin Bedő +# +# Permission to use, copy, modify, and/or distribute this software for any +# purpose with or without fee is hereby granted, provided that the above +# copyright notice and this permission notice appear in all copies. +# +# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES +# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR +# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES +# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN +# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF +# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + +pmt <- function(a, b, two.sided=F) { + ce <- function(mu){ + pt1 <- mapply(function(xa, mu, rho) logsumexp(cumsum(log(((1 + rho) * (xa - (0:xa-1))/(2 * mu))))), a, mu, rho) + pt2 <- mapply(function(xb, mu, rho) logsumexp(cumsum(log((2*mu*rho) / ((1 + rho)*(xb + (1:100)))))), b, mu, rho) + rho + rho * (exp(pt1) - exp(pt2)) + } + + logsumexp <- function(x) { + x <- sort(x, decreasing=T) + log1p(sum(exp(x[-1] - x[1]))) + x[1] + } + + Ra <- sum(a) + Rb <- sum(b) + chi <- a/b + rho <- rep(Ra/Rb, length(a)) + + msk <- a/Ra > b/Rb + rho[msk] <- 1/rho[msk] + tmp <- a[msk] + a[msk] <- b[msk] + b[msk] <- tmp + chi[msk] <- 1/chi[msk] + + lb <- (rho - chi + sqrt(((rho - chi)^2 + 4 * chi * rho * (1 + rho)))) / (4 * rho) * b * 0.75 + ub <- (1 + chi) * (1 + rho) / (2 * rho + 1) * b * 1.25 + + while(max(ub - lb) > 1e-6){ + mu <- (ub + lb) / 2 + scmu <- ce(mu) >= 0 + ub <- ub * scmu + mu * (1 - scmu) + lb <- lb * (1 - scmu) + mu * scmu + } + + t1 <- mapply(function(xa, mu, rho) { i <- 0:xa; logsumexp(i * log(2 * mu) - lfactorial(i) - i * log(1 + rho))}, a, mu, rho) + t2 <- mapply(function(xb, mu, rho) { j <- xb:(xb*100); logsumexp(j * log(2 * mu * rho) - lfactorial(j) - j * log(1 + rho))}, b, mu, rho) + + (2*mu-t1-t2) / log(10) +} diff --git a/man/pmt-package.Rd b/man/pmt-package.Rd new file mode 100644 index 0000000..5c653d1 --- /dev/null +++ b/man/pmt-package.Rd @@ -0,0 +1,26 @@ +\name{pmt-package} +\alias{pmt-package} +\alias{pmt} +\docType{package} +\title{ +\packageTitle{pmt} +Poisson Margin Test +} +\description{ +\packageDescription{pmt} +Computes p-values using the Poission Margin Test for two vectors of counts arising from NGS data. +} +\details{ +\packageDESCRIPTION{pmt} +\packageIndices{pmt} +} +\author{ +\packageAuthor{pmt} + +Maintainer: \packageMaintainer{pmt} +} +\references{ +Kowalczyk, A., Bedő, J., Conway, T., Beresford-Smith, B., 2011. The Poisson margin test for normalization-free significance analysis of NGS data. Journal of Computational Biology 18, 391–400. doi:10.1089/cmb.2010.0272 +} +\keyword{NGS} +\keyword{Poisson} diff --git a/man/pmt.Rd b/man/pmt.Rd new file mode 100644 index 0000000..c9e0250 --- /dev/null +++ b/man/pmt.Rd @@ -0,0 +1,33 @@ +\name{pmt} +\alias{pmt} +\title{Poisson Margin Test} +\description{ + Computes p-values for two sets of counts using the Poisson Margin Test. +} +\usage{ +pmt(a, b) +} +\arguments{ + \item{a}{ + Vector of counts +} + \item{b}{ + Vector of counts +} +} +\details{ + This function computes the Poisson Margin Test (PMT) for two sets of counts. +} +\value{ + A vector of log10 p-values is returned, corresponding to the input vectors. +} +\references{ +Kowalczyk, A., Bedő, J., Conway, T., Beresford-Smith, B., 2011. The Poisson margin test for normalization-free significance analysis of NGS data. Journal of Computational Biology 18, 391–400. doi:10.1089/cmb.2010.0272 +} +\author{ + Justin Bedő +} +%\examples{ +%} +\keyword{NGS} +\keyword{Poisson} -- cgit v1.2.3