atMPRA-package: Analysis Toolset for MPRA data
In redaq/atMPRA: Analysis Toolset for MPRA data

Description Details Author(s) References See Also Examples

Includes the adaptive test and a number of other methods for analyzing MPRA data, and also functions for power calculation for designing MPRA experiments. The adaptive method is described in Qiao, D., Zigler, C., Cho, M.H., Silverman, E.K., Zhou, X., et al. (2018). Statistical considerations for the analysis of massively parallel reporter assays data.

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This package implements the adaptive test and a number of other methods for analyzing MPRA data, and also functions of power calculations for the design of MPRA experiments. The main functions are: getPower: function for power calculation using simulated data and specified test sim_fixInputDist: function for simulating MPRA data with specified mean and standard deviation for the input distributions sim_fixTotalD: function for simulating MPRA data with specified input distribution and total depth sim_fixMeanD: function for simulating MPRA data with specified input distribution and mean depth analyzeMPRA: function for analyzing MPRA data (either real or simulated) using specified test

Dandi Qiao, Peter J. Castaldi

Maintainer: Dandi Qiao <redaq@channing.harvard.edu>

Qiao, D., Zigler, C., Cho, M.H., Silverman, E.K., Zhou, X., et al. (2018). Statistical considerations for the analysis of massively parallel reporter assays data.

atMPRA

nsim = 10
ntag = 10
slope=c(rep(1, ntag*nsim), rep(1.5, ntag*nsim)) 
results = getPower(nsim = nsim, ntag = ntag, nrep = 1, slope=slope , scenario=c("fixInputDist"), method="MW", sigma2_DNA_a0=0.001, sigma2_DNA_a1=0.23, sigma2_RNA_a0=0.18, sigma2_RNA_a1=35, fixInput  = c(20, 120, 20, 120))

nrep=5
data(datMean)
simData = sim_fixTotalD(datMean=datMean, totalDepth=200000, sigma2_DNA_a0=0.001, sigma2_DNA_a1=0.23, sigma2_RNA_a0=0.18, sigma2_RNA_a1=35, ntag=ntag, nsim=nsim, nrep=nrep, slope=slope)

results2 = analyzeMPRA(simData, nrep, rnaCol=2+nrep+1, nrep, nsim, ntag, method=c("MW","mpralm", "edgeR", "DESeq2"), cutoff=0, cutoffo=0)