added eQTL functions to manual section

man/splateQTL.Rd

@@ -14,7 +14,6 @@ splateQTL(
   eqtl.dist = 1e+06,
   eqtl.maf = 0.1,
   eqtl.mafd = 0.01,
-  eqtl.bcv = 0.4,
   eqtl.save = TRUE,
   ...
 )
@@ -23,7 +22,7 @@ splateQTL(
 \item{params}{SplatParams object containing parameters for the simulation.
 See \code{\link{SplatParams}} for details.}
 
-\item{gff_file}{Path to a GFF/GFT file containing genes to include.}
+\item{gff_file}{Path to a GFF/GTF file containing genes to include.}
 
 \item{snp_file}{Path to real/simulated genotype data in .vcf format. 
 Where each column is a sample and each row is a SNP.}
@@ -42,8 +41,6 @@ GTEx thyroid cis-eQTL data)}
 
 \item{eqtl.mafd}{Maximum variation from eqtl.maf to include as eSNP}
 
-\item{eqtl.bcv}{Biological Coefficient of Variation (default = 0.4)}
-
 \item{eqtl.save}{logical. Whether to save eQTL key and mean matrix.}
 
 \item{...}{any additional parameter settings to override what is provided in
@@ -56,8 +53,8 @@ intermediate values.
 }
 \description{
 Simulate mean gene counts for a population of samples, such that a defined 
-number of associations (i.e. cis-eQTL) between markers (i.e. eSNPs) and genes 
-(i.e. eGenes) exist.
+number of associations (cis-eQTL) between markers (eSNPs) and genes 
+(eGenes) exist.
 }
 \details{
 Parameters can be set in a variety of ways. If no parameters are provided
@@ -75,7 +72,7 @@ The eQTL Gene Mean simulation involves the following steps:
     \item Generate normalized gene mean expression matrix for the population. 
     \item Set a gene mean expression value (not normalized) for each gene. 
     \item Generate a gene mean expression matrix for the population.
-    \item (optional) Save eQTL key (i.e. pairs)
+    \item (optional) Save eQTL key (pairs)
 }
 }
 \examples{

man/splateQTLGeneMeans.Rd

@@ -4,10 +4,11 @@
 \alias{splateQTLGeneMeans}
 \title{Set a gene mean expression value (not normalized) for each gene.}
 \usage{
-splateQTLGeneMeans(params, pairs, eqtl.bcv)
+splateQTLGeneMeans(params, pairs)
 }
 \arguments{
-\item{params}{Output from splateQTL_DefineAssociations}
+\item{params}{SplatParams object containing parameters for the simulation.
+See \code{\link{SplatParams}} for details.}
 
 \item{pairs}{A dataframe eSNPs-eGenes pair assignments and their effect sizes}
 }

man/splateQTLMeansMatrix.Rd

@@ -2,24 +2,27 @@
 % Please edit documentation in R/splat-eqtl.R
 \name{splateQTLMeansMatrix}
 \alias{splateQTLMeansMatrix}
-\title{Un-normalize the mean gene expression matrix}
+\title{Project normalized gene expression matrix into mean gene expression matrix}
 \usage{
-splateQTLMeansMatrix(pairs, nMeans)
+splateQTLMeansMatrix(params, pairs, nMeans)
 }
 \arguments{
-\item{nMeans}{The normalized gene expression means for the population}
+\item{params}{SplatParams object containing parameters for the simulation.
+See \code{\link{SplatParams}} for details.}
+
+\item{pairs}{A dataframe eSNPs-eGenes pair assignments and their effect sizes}
 
-\item{params}{A dataframe eSNPs-eGenes pair assignments and their effect sizes}
+\item{nMeans}{The normalized gene expression means for the population}
 }
 \value{
 MeansMatrix: Matrix of simulated gene means for eQTL population.
 }
 \description{
-Un-normalize the mean gene expression matrix
+Project normalized gene expression matrix into mean gene expression matrix
 }
 \details{
 For each gene/sample, the normalized expression value (from rnorm) is 
 transformed to the cumulative density function (pnorm) between 0 and 1, this
-value is then inversed (qnorm) to map the probability to a value defined by
-the gene mean assigned in splateQTLGeneMeans.
+value is then quantile normalized (qgamma) using the gamma distribution 
+parameterized from splatEstimate().
 }

man/splateQTLgenes.Rd

@@ -13,7 +13,7 @@ splateQTLgenes(gff_file)
 A dataframe containing gene IDs and locations.
 }
 \description{
-Read in GFF/GTF file (ignorning header) and select only sequences where the 
+Read in GFF/GTF file (ignoring header) and select only sequences where the 
 feature is listed as a gene. Then get the Transcriptional Start Site for 
 each gene (depending on strand direction).
 }

man/splateQTLpairs.Rd

@@ -27,6 +27,6 @@ A dataframe eSNPs-eGenes pair assignments and their effect sizes
 \description{
 Randomly pairs N eSNPs with an eGene within the designated window size 
 (eqtl.dist) and assigns each pair an effect size sampled from a gamma 
-distribution parameterized using the effect sizes from a builk eQTL study 
+distribution parameterized using the effect sizes from a bulk eQTL study 
 using the GTEx data from the thyroid tissue.
 }

man/splateQTLsnps.Rd

@@ -7,7 +7,7 @@
 splateQTLsnps(snp_file, eqtl.maf, eqtl.mafd)
 }
 \arguments{
-\item{snp_file}{Path to real/simulated genotype data in .ped.gen format}
+\item{snp_file}{Path to real/simulated genotype data (.vcf)}
 
 \item{eqtl.maf}{Desired Minor Allele Frequency (MAF) of eSNPs to include}