diff --git a/man/ratiometric.bbd.power.Rd b/man/ratiometric.bbd.power.Rd
index 7f0af2b..2c64be1 100644
--- a/man/ratiometric.bbd.power.Rd
+++ b/man/ratiometric.bbd.power.Rd
@@ -6,7 +6,7 @@
 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)
+  r = 0.02, signif.level = 5e-06, nonsil.frac = 3/4)
 }
 \arguments{
 \item{my.alpha}{alpha parameter for beta binomial}
@@ -17,11 +17,16 @@ ratiometric.bbd.power(my.alpha, my.beta, N, mu, Df = 1, Leff = 1500 * 3/4,
 
 \item{mu}{per base rate of mutation}
 
-\item{Leff}{length of gene in bases}
+\item{Df}{Fraction of driver mutations which are relavent to 
+the ratio-metric feature of interest.}
+
+\item{Leff}{effective length of gene in bases (Length*nonsil.frac)}
 
 \item{r}{effect size for power analysis}
 
 \item{signif.level}{alpha level for power analysis}
+
+\item{nonsil.frac}{fraction of mutations which are non-silent}
 }
 \value{
 vector containing power for each sample size
diff --git a/man/ratiometric.binom.false.pos.Rd b/man/ratiometric.binom.false.pos.Rd
index 3b8bd33..efa8520 100644
--- a/man/ratiometric.binom.false.pos.Rd
+++ b/man/ratiometric.binom.false.pos.Rd
@@ -6,7 +6,7 @@
 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)
+  num.genes = 18500, signif.level = 5e-06, nonsil.frac = 3/4)
 }
 \arguments{
 \item{my.alpha}{alpha parameter for beta binomial}
@@ -17,11 +17,16 @@ ratiometric.binom.false.pos(my.alpha, my.beta, N, mu, Leff = 1500 * 3/4,
 
 \item{mu}{mutation rate per base}
 
+\item{Leff}{efective gene CDS length in bases}
+
 \item{num.genes}{number of genes that are tested}
 
 \item{signif.level}{alpha level for power analysis}
 
-\item{L}{gene CDS length in bases}
+\item{nonsil.frac}{fraction of mutations which are non-silent}
+}
+\value{
+vector containing expected false positive genes
 }
 \description{
 calculates the false positives for a binomial model of
diff --git a/man/ratiometric.binom.power.Rd b/man/ratiometric.binom.power.Rd
index 14fac34..c6b7981 100644
--- a/man/ratiometric.binom.power.Rd
+++ b/man/ratiometric.binom.power.Rd
@@ -6,7 +6,7 @@
 for ratio-metric approach}
 \usage{
 ratiometric.binom.power(p, N, mu, Df = 1, Leff = 1500 * 3/4, r = 0.02,
-  signif.level = 5e-06)
+  signif.level = 5e-06, nonsil.frac = 3/4)
 }
 \arguments{
 \item{p}{background proportion of total mutations falling into specific category}
@@ -17,11 +17,13 @@ ratiometric.binom.power(p, N, mu, Df = 1, Leff = 1500 * 3/4, r = 0.02,
 
 \item{Df}{fraction of driver mutations that are the specific one of interest}
 
-\item{Leff}{gene length in bases}
+\item{Leff}{effective gene length in bases (Length*nonsil.frac)}
 
 \item{r}{effect size for power analysis}
 
 \item{signif.level}{alpha level for power analysis}
+
+\item{nonsil.frac}{fraction of mutations which are non-silent}
 }
 \value{
 vector containing power for each sample size
diff --git a/man/ratiometricBbdPoweredEffectSize.Rd b/man/ratiometricBbdPoweredEffectSize.Rd
index 6d93f5d..2330bd2 100644
--- a/man/ratiometricBbdPoweredEffectSize.Rd
+++ b/man/ratiometricBbdPoweredEffectSize.Rd
@@ -21,6 +21,8 @@ ratiometricBbdPoweredEffectSize(possible.effect.sizes, desired.power, p, cv, mu,
 
 \item{samp.size}{number of cancer samples in study}
 
+\item{Df}{fraction of driver mutations that are the specific one of interest}
+
 \item{signif.level}{significance level for binomial test}
 
 \item{Leff}{effective gene length of CDS in bases for an average gene}
diff --git a/man/ratiometricBbdRequiredSampleSize.Rd b/man/ratiometricBbdRequiredSampleSize.Rd
index 92d337f..fb40e43 100644
--- a/man/ratiometricBbdRequiredSampleSize.Rd
+++ b/man/ratiometricBbdRequiredSampleSize.Rd
@@ -21,9 +21,11 @@ ratiometricBbdRequiredSampleSize(p, cv, desired.power, possible.samp.sizes, mu,
 
 \item{effect.size}{fraction of samples above background mutation rate}
 
-\item{signif.level}{significance level for binomial test}
+\item{Df}{fraction of driver mutations that are the specific one of interest}
 
-\item{L}{gene length of CDS in bases for an average gene}
+\item{signif.lvl}{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
diff --git a/man/ratiometricBinomPoweredEffectSize.Rd b/man/ratiometricBinomPoweredEffectSize.Rd
index ee7608d..22371a6 100644
--- a/man/ratiometricBinomPoweredEffectSize.Rd
+++ b/man/ratiometricBinomPoweredEffectSize.Rd
@@ -19,6 +19,8 @@ ratiometricBinomPoweredEffectSize(possible.effect.sizes, desired.power, p, mu,
 
 \item{samp.size}{number of cancer samples in study}
 
+\item{Df}{fraction of driver mutations that are the specific one of interest}
+
 \item{signif.level}{significance level for binomial test}
 
 \item{Leff}{effective gene length of CDS in bases for an average gene}
diff --git a/man/ratiometricBinomRequiredSampleSize.Rd b/man/ratiometricBinomRequiredSampleSize.Rd
index cdf9ee2..fa86f67 100644
--- a/man/ratiometricBinomRequiredSampleSize.Rd
+++ b/man/ratiometricBinomRequiredSampleSize.Rd
@@ -19,9 +19,11 @@ ratiometricBinomRequiredSampleSize(p, desired.power, possible.samp.sizes, mu,
 
 \item{effect.size}{fraction of samples above background mutation rate}
 
-\item{signif.level}{significance level for binomial test}
+\item{Df}{fraction of driver mutations that are the specific one of interest}
 
-\item{L}{gene length of CDS in bases for an average gene}
+\item{signif.lvl}{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