diff --git a/man/ratiometric.bbd.power.Rd b/man/ratiometric.bbd.power.Rd
new file mode 100644
index 0000000..7f0af2b
--- /dev/null
+++ b/man/ratiometric.bbd.power.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ratioMetric.R
+\name{ratiometric.bbd.power}
+\alias{ratiometric.bbd.power}
+\title{Calculates the power in a ratio-metric approach using 
+a beta-binomial power model.}
+\usage{
+ratiometric.bbd.power(my.alpha, my.beta, N, mu, Df = 1, Leff = 1500 * 3/4,
+  r = 0.02, signif.level = 5e-06)
+}
+\arguments{
+\item{my.alpha}{alpha parameter for beta binomial}
+
+\item{my.beta}{beta parameter for beta binomial}
+
+\item{N}{vector of sample sizes}
+
+\item{mu}{per base rate of mutation}
+
+\item{Leff}{length of gene in bases}
+
+\item{r}{effect size for power analysis}
+
+\item{signif.level}{alpha level for power analysis}
+}
+\value{
+vector containing power for each sample size
+}
+\description{
+The alpha and beta parameterize a proportion out of the
+total mutations in a gene, rather than a mutation rate per base.
+}
+
diff --git a/man/ratiometric.binom.false.pos.Rd b/man/ratiometric.binom.false.pos.Rd
new file mode 100644
index 0000000..3b8bd33
--- /dev/null
+++ b/man/ratiometric.binom.false.pos.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ratioMetric.R
+\name{ratiometric.binom.false.pos}
+\alias{ratiometric.binom.false.pos}
+\title{calculates the false positives for a binomial model of
+a ratio-metric feature.}
+\usage{
+ratiometric.binom.false.pos(my.alpha, my.beta, N, mu, Leff = 1500 * 3/4,
+  num.genes = 18500, signif.level = 5e-06)
+}
+\arguments{
+\item{my.alpha}{alpha parameter for beta binomial}
+
+\item{my.beta}{beta parameter for beta binomial}
+
+\item{N}{vector of # samples to calculate power for}
+
+\item{mu}{mutation rate per base}
+
+\item{num.genes}{number of genes that are tested}
+
+\item{signif.level}{alpha level for power analysis}
+
+\item{L}{gene CDS length in bases}
+}
+\description{
+calculates the false positives for a binomial model of
+a ratio-metric feature.
+}
+
diff --git a/man/ratiometric.binom.power.Rd b/man/ratiometric.binom.power.Rd
new file mode 100644
index 0000000..14fac34
--- /dev/null
+++ b/man/ratiometric.binom.power.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ratioMetric.R
+\name{ratiometric.binom.power}
+\alias{ratiometric.binom.power}
+\title{calculates the power in a binomial power model
+for ratio-metric approach}
+\usage{
+ratiometric.binom.power(p, N, mu, Df = 1, Leff = 1500 * 3/4, r = 0.02,
+  signif.level = 5e-06)
+}
+\arguments{
+\item{p}{background proportion of total mutations falling into specific category}
+
+\item{N}{vector of sample sizes}
+
+\item{mu}{per base rate of mutation}
+
+\item{Df}{fraction of driver mutations that are the specific one of interest}
+
+\item{Leff}{gene length in bases}
+
+\item{r}{effect size for power analysis}
+
+\item{signif.level}{alpha level for power analysis}
+}
+\value{
+vector containing power for each sample size
+}
+\description{
+calculates the power in a binomial power model
+for ratio-metric approach
+}
+
diff --git a/man/ratiometricBbdPoweredEffectSize.Rd b/man/ratiometricBbdPoweredEffectSize.Rd
new file mode 100644
index 0000000..6d93f5d
--- /dev/null
+++ b/man/ratiometricBbdPoweredEffectSize.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ratioMetric.R
+\name{ratiometricBbdPoweredEffectSize}
+\alias{ratiometricBbdPoweredEffectSize}
+\title{Calculates the effect size of a driver gene according to a beta-binomial model
+of ratio-metric features for which there is sufficient power.}
+\usage{
+ratiometricBbdPoweredEffectSize(possible.effect.sizes, desired.power, p, cv, mu,
+  samp.size, Df = 1, signif.level = 5e-06, Leff = 1500 * 3/4)
+}
+\arguments{
+\item{possible.effect.sizes}{vector of effect sizes}
+
+\item{desired.power}{A floating point number indicating desired power}
+
+\item{p}{the background fraction of total mutations represented by the ratio-metric feature (e.g. inactivating mutations / total)}
+
+\item{cv}{the coefficient of variation for the parameter p}
+
+\item{mu}{Mutation rate per base}
+
+\item{samp.size}{number of cancer samples in study}
+
+\item{signif.level}{significance level for binomial test}
+
+\item{Leff}{effective gene length of CDS in bases for an average gene}
+}
+\value{
+List containing the smallest effect size with sufficient power
+}
+\description{
+Effect size is measures as the fraction of sample/patient cancers with a 
+mutation in a driver gene above the background mutation rate.
+}
+
diff --git a/man/ratiometricBbdRequiredSampleSize.Rd b/man/ratiometricBbdRequiredSampleSize.Rd
new file mode 100644
index 0000000..92d337f
--- /dev/null
+++ b/man/ratiometricBbdRequiredSampleSize.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ratioMetric.R
+\name{ratiometricBbdRequiredSampleSize}
+\alias{ratiometricBbdRequiredSampleSize}
+\title{Calculates the smallest sample size to detect driver genes for which
+there is sufficient power using a beta-binomial model for ratio-metric features.}
+\usage{
+ratiometricBbdRequiredSampleSize(p, cv, desired.power, possible.samp.sizes, mu,
+  effect.size, Df = 1, signif.lvl = 5e-06, Leff = 1500 * 3/4)
+}
+\arguments{
+\item{p}{the background fraction of total mutations represented by the ratio-metric feature (e.g. inactivating mutations / total)}
+
+\item{cv}{the coefficient of variation for the parameter p}
+
+\item{desired.power}{A floating point number indicating desired power}
+
+\item{possible.samp.sizes}{vector of possible number of cancer samples in study}
+
+\item{mu}{mutation rate per base}
+
+\item{effect.size}{fraction of samples above background mutation rate}
+
+\item{signif.level}{significance level for binomial test}
+
+\item{L}{gene length of CDS in bases for an average gene}
+}
+\value{
+List containing the smallest effect size with sufficient power
+}
+\description{
+Effect size is measures as the fraction of sample/patient cancers with a non-silent
+mutation in a driver gene above the background mutation rate.
+}
+
diff --git a/man/ratiometricBinomPoweredEffectSize.Rd b/man/ratiometricBinomPoweredEffectSize.Rd
new file mode 100644
index 0000000..ee7608d
--- /dev/null
+++ b/man/ratiometricBinomPoweredEffectSize.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ratioMetric.R
+\name{ratiometricBinomPoweredEffectSize}
+\alias{ratiometricBinomPoweredEffectSize}
+\title{Calculates the effect size of a driver gene according to a binomial model
+of ratio-metric features for which there is sufficient power.}
+\usage{
+ratiometricBinomPoweredEffectSize(possible.effect.sizes, desired.power, p, mu,
+  samp.size, Df = 1, signif.level = 5e-06, Leff = 1500 * 3/4)
+}
+\arguments{
+\item{possible.effect.sizes}{vector of effect sizes}
+
+\item{desired.power}{A floating point number indicating desired power}
+
+\item{p}{the background fraction of total mutations represented by the ratio-metric feature (e.g. inactivating mutations / total)}
+
+\item{mu}{Mutation rate per base}
+
+\item{samp.size}{number of cancer samples in study}
+
+\item{signif.level}{significance level for binomial test}
+
+\item{Leff}{effective gene length of CDS in bases for an average gene}
+}
+\value{
+List containing the smallest effect size with sufficient power
+}
+\description{
+Effect size is measures as the fraction of sample/patient cancers with a 
+mutation in a driver gene above the background mutation rate.
+}
+
diff --git a/man/ratiometricBinomRequiredSampleSize.Rd b/man/ratiometricBinomRequiredSampleSize.Rd
new file mode 100644
index 0000000..cdf9ee2
--- /dev/null
+++ b/man/ratiometricBinomRequiredSampleSize.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ratioMetric.R
+\name{ratiometricBinomRequiredSampleSize}
+\alias{ratiometricBinomRequiredSampleSize}
+\title{Calculates the smallest sample size to detect driver genes for which
+there is sufficient power using a binomial model for ratio-metric features.}
+\usage{
+ratiometricBinomRequiredSampleSize(p, desired.power, possible.samp.sizes, mu,
+  effect.size, Df = 1, signif.lvl = 5e-06, Leff = 1500 * 3/4)
+}
+\arguments{
+\item{p}{the background fraction of total mutations represented by the ratio-metric feature (e.g. inactivating mutations / total)}
+
+\item{desired.power}{A floating point number indicating desired power}
+
+\item{possible.samp.sizes}{vector of possible number of cancer samples in study}
+
+\item{mu}{mutation rate per base}
+
+\item{effect.size}{fraction of samples above background mutation rate}
+
+\item{signif.level}{significance level for binomial test}
+
+\item{L}{gene length of CDS in bases for an average gene}
+}
+\value{
+List containing the smallest effect size with sufficient power
+}
+\description{
+Effect size is measures as the fraction of sample/patient cancers with a non-silent
+mutation in a driver gene above the background mutation rate.
+}
+
diff --git a/man/runAnalysisList.Rd b/man/runAnalysisList.Rd
index 01a9984..36811bc 100644
--- a/man/runAnalysisList.Rd
+++ b/man/runAnalysisList.Rd
@@ -7,8 +7,7 @@ rate, effect.size, and significance level. The purpose of this function is paral
 code running over a list of parameters. If you are not parallelizing, then use the 
 runAnalysis function.}
 \usage{
-runAnalysisList(x, samp.sizes, desired.power = 0.9, Leff = 1500 * 3/4,
-  possible.cvs = c())
+runAnalysisList(x, analysisType = "smg", Leff = 1500 * 3/4, Df = 1, ...)
 }
 \description{
 This function unpacks a vector x which contains many combinations of the mutation
diff --git a/man/runRatiometricAnalysis.Rd b/man/runRatiometricAnalysis.Rd
new file mode 100644
index 0000000..990cb67
--- /dev/null
+++ b/man/runRatiometricAnalysis.Rd
@@ -0,0 +1,13 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cancerSeqStudy.R
+\name{runRatiometricAnalysis}
+\alias{runRatiometricAnalysis}
+\title{Runs the entire power and false positive analysis pipeline.}
+\usage{
+runRatiometricAnalysis(p, mu, effect.size, signif.level, samp.sizes,
+  desired.power = 0.9, Leff = 1500 * 3/4, Df = 1, possible.cvs = c())
+}
+\description{
+Runs the entire power and false positive analysis pipeline.
+}
+
diff --git a/man/runAnalysis.Rd b/man/runSmgAnalysis.Rd
similarity index 70%
rename from man/runAnalysis.Rd
rename to man/runSmgAnalysis.Rd
index bdb16c9..8d32b6d 100644
--- a/man/runAnalysis.Rd
+++ b/man/runSmgAnalysis.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/cancerSeqStudy.R
-\name{runAnalysis}
-\alias{runAnalysis}
+\name{runSmgAnalysis}
+\alias{runSmgAnalysis}
 \title{Runs the entire power and false positive analysis pipeline.}
 \usage{
-runAnalysis(pi, effect.size, signif.level, samp.sizes, desired.power = 0.9,
+runSmgAnalysis(mu, effect.size, signif.level, samp.sizes, desired.power = 0.9,
   Leff = 1500 * 3/4, possible.cvs = c())
 }
 \description{
diff --git a/man/bbd.power.Rd b/man/smg.bbd.power.Rd
similarity index 56%
rename from man/bbd.power.Rd
rename to man/smg.bbd.power.Rd
index ea43e84..05707b8 100644
--- a/man/bbd.power.Rd
+++ b/man/smg.bbd.power.Rd
@@ -1,10 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cancerSeqStudy.R
-\name{bbd.power}
-\alias{bbd.power}
-\title{calculates the power in a beta-binomial model}
+% Please edit documentation in R/smg.R
+\name{smg.bbd.power}
+\alias{smg.bbd.power}
+\title{calculates the power in a beta-binomial model for
+significantly mutated genes.}
 \usage{
-bbd.power(my.alpha, my.beta, N, Leff = 1500 * 3/4, r = 0.02,
+smg.bbd.power(my.alpha, my.beta, N, Leff = 1500 * 3/4, r = 0.02,
   signif.level = 5e-06)
 }
 \arguments{
@@ -21,6 +22,7 @@ bbd.power(my.alpha, my.beta, N, Leff = 1500 * 3/4, r = 0.02,
 \item{signif.level}{alpha level for power analysis}
 }
 \description{
-calculates the power in a beta-binomial model
+calculates the power in a beta-binomial model for
+significantly mutated genes.
 }
 
diff --git a/man/binom.false.pos.Rd b/man/smg.binom.false.pos.Rd
similarity index 58%
rename from man/binom.false.pos.Rd
rename to man/smg.binom.false.pos.Rd
index 8c46f8c..fbff2f8 100644
--- a/man/binom.false.pos.Rd
+++ b/man/smg.binom.false.pos.Rd
@@ -1,12 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cancerSeqStudy.R
-\name{binom.false.pos}
-\alias{binom.false.pos}
+% Please edit documentation in R/smg.R
+\name{smg.binom.false.pos}
+\alias{smg.binom.false.pos}
 \title{calculates the false positives in a binomial model
-if there is over-diserspion}
+for identifying significantly mutated genes if 
+there is over-diserspion.}
 \usage{
-binom.false.pos(my.alpha, my.beta, N, Leff = 1500 * 3/4, num.genes = 18500,
-  signif.level = 5e-06)
+smg.binom.false.pos(my.alpha, my.beta, N, Leff = 1500 * 3/4,
+  num.genes = 18500, signif.level = 5e-06)
 }
 \arguments{
 \item{my.alpha}{alpha parameter for beta binomial}
@@ -23,6 +24,7 @@ binom.false.pos(my.alpha, my.beta, N, Leff = 1500 * 3/4, num.genes = 18500,
 }
 \description{
 calculates the false positives in a binomial model
-if there is over-diserspion
+for identifying significantly mutated genes if 
+there is over-diserspion.
 }
 
diff --git a/man/binom.power.Rd b/man/smg.binom.power.Rd
similarity index 56%
rename from man/binom.power.Rd
rename to man/smg.binom.power.Rd
index bb85eae..65bceec 100644
--- a/man/binom.power.Rd
+++ b/man/smg.binom.power.Rd
@@ -1,10 +1,12 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cancerSeqStudy.R
-\name{binom.power}
-\alias{binom.power}
-\title{calculates the power in a binomial power model}
+% Please edit documentation in R/smg.R
+\name{smg.binom.power}
+\alias{smg.binom.power}
+\title{calculates the power in a binomial power model
+for significantly mutated genes}
 \usage{
-binom.power(my.mu, N, Leff = 1500 * 3/4, r = 0.02, signif.level = 5e-06)
+smg.binom.power(my.mu, N, Leff = 1500 * 3/4, r = 0.02,
+  signif.level = 5e-06)
 }
 \arguments{
 \item{my.mu}{per base rate of mutation for binomial}
@@ -20,5 +22,6 @@ vector containing power for each sample size
 }
 \description{
 calculates the power in a binomial power model
+for significantly mutated genes
 }
 
diff --git a/man/bbdPoweredEffectSize.Rd b/man/smgBbdPoweredEffectSize.Rd
similarity index 74%
rename from man/bbdPoweredEffectSize.Rd
rename to man/smgBbdPoweredEffectSize.Rd
index 23654fb..e174b43 100644
--- a/man/bbdPoweredEffectSize.Rd
+++ b/man/smgBbdPoweredEffectSize.Rd
@@ -1,11 +1,12 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cancerSeqStudy.R
-\name{bbdPoweredEffectSize}
-\alias{bbdPoweredEffectSize}
+% Please edit documentation in R/smg.R
+\name{smgBbdPoweredEffectSize}
+\alias{smgBbdPoweredEffectSize}
 \title{Calculates the smallest effect size in a driver gene for which
-there is sufficient power using a beta-binomial model.}
+there is sufficient power using a significantly mutated gene
+approach with a beta-binomial model.}
 \usage{
-bbdPoweredEffectSize(possible.effect.sizes, desired.power, mu, cv, samp.size,
+smgBbdPoweredEffectSize(possible.effect.sizes, desired.power, mu, cv, samp.size,
   signif.level = 5e-06, Leff = 1500 * 3/4)
 }
 \arguments{
diff --git a/man/bbdRequiredSampleSize.Rd b/man/smgBbdRequiredSampleSize.Rd
similarity index 79%
rename from man/bbdRequiredSampleSize.Rd
rename to man/smgBbdRequiredSampleSize.Rd
index a5eff89..d1ae322 100644
--- a/man/bbdRequiredSampleSize.Rd
+++ b/man/smgBbdRequiredSampleSize.Rd
@@ -1,12 +1,12 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cancerSeqStudy.R
-\name{bbdRequiredSampleSize}
-\alias{bbdRequiredSampleSize}
+% Please edit documentation in R/smg.R
+\name{smgBbdRequiredSampleSize}
+\alias{smgBbdRequiredSampleSize}
 \title{Calculates the smallest sample size to detect driver genes for which
 there is sufficient power using a beta-binomial model.}
 \usage{
-bbdRequiredSampleSize(desired.power, mu, cv, possible.samp.sizes, effect.size,
-  signif.level = 5e-06, Leff = 1500 * 3/4)
+smgBbdRequiredSampleSize(desired.power, mu, cv, possible.samp.sizes,
+  effect.size, signif.level = 5e-06, Leff = 1500 * 3/4)
 }
 \arguments{
 \item{desired.power}{A floating point number indicating desired power}
diff --git a/man/binomPoweredEffectSize.Rd b/man/smgBinomPoweredEffectSize.Rd
similarity index 67%
rename from man/binomPoweredEffectSize.Rd
rename to man/smgBinomPoweredEffectSize.Rd
index 6c9972d..8177966 100644
--- a/man/binomPoweredEffectSize.Rd
+++ b/man/smgBinomPoweredEffectSize.Rd
@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cancerSeqStudy.R
-\name{binomPoweredEffectSize}
-\alias{binomPoweredEffectSize}
-\title{Calculates the effect size of a driver gene according to a binomial for which
-there is sufficient power.}
+% Please edit documentation in R/smg.R
+\name{smgBinomPoweredEffectSize}
+\alias{smgBinomPoweredEffectSize}
+\title{Calculates the minimum effect size (with sufficient power) of a driver gene according to a binomial model 
+for significantly mutated genes.}
 \usage{
-binomPoweredEffectSize(possible.effect.sizes, desired.power, mu, samp.size,
+smgBinomPoweredEffectSize(possible.effect.sizes, desired.power, mu, samp.size,
   signif.level = 5e-06, Leff = 1500 * 3/4)
 }
 \arguments{
diff --git a/man/binomRequiredSampleSize.Rd b/man/smgBinomRequiredSampleSize.Rd
similarity index 76%
rename from man/binomRequiredSampleSize.Rd
rename to man/smgBinomRequiredSampleSize.Rd
index fe6336e..008e6f9 100644
--- a/man/binomRequiredSampleSize.Rd
+++ b/man/smgBinomRequiredSampleSize.Rd
@@ -1,11 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cancerSeqStudy.R
-\name{binomRequiredSampleSize}
-\alias{binomRequiredSampleSize}
+% Please edit documentation in R/smg.R
+\name{smgBinomRequiredSampleSize}
+\alias{smgBinomRequiredSampleSize}
 \title{Calculates the smallest sample size to detect driver genes for which
-there is sufficient power using a binomial model.}
+there is sufficient power using a binomial model for mutation rate.}
 \usage{
-binomRequiredSampleSize(desired.power, mu, possible.samp.sizes, effect.size,
+smgBinomRequiredSampleSize(desired.power, mu, possible.samp.sizes, effect.size,
   signif.level = 5e-06, Leff = 1500 * 3/4)
 }
 \arguments{
diff --git a/man/thisfile.Rd b/man/thisfile.Rd
new file mode 100644
index 0000000..5c31559
--- /dev/null
+++ b/man/thisfile.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cancerSeqStudy.R
+\name{thisfile}
+\alias{thisfile}
+\title{Utility function to get location of script when
+executing Rscript.}
+\usage{
+thisfile()
+}
+\description{
+Utility function to get location of script when
+executing Rscript.
+}
+