From bbc1ca289a4a048ca56072a34e2675816dd75074 Mon Sep 17 00:00:00 2001
From: cazodi <cazodi@svi.edu.au>
Date: Tue, 28 Jan 2020 12:15:53 +1100
Subject: [PATCH] skill install
---
.travis.yml | 3 +-
DESCRIPTION | 2 +-
man/BASiCSEstimate.Rd | 50 ++++++++++++++----
man/addFeatureStats.Rd | 9 +++-
man/addGeneLengths.Rd | 9 +++-
man/compareSCEs.Rd | 9 +++-
man/diffSCEs.Rd | 10 +++-
man/expandParams.Rd | 1 -
man/getParam.Rd | 1 -
man/kersplatEstimate.Rd | 6 +--
man/lun2Estimate.Rd | 31 ++++++++---
man/lun2Simulate.Rd | 3 +-
man/lunEstimate.Rd | 3 +-
man/makeCompPanel.Rd | 9 ++--
man/makeDiffPanel.Rd | 10 ++--
man/makeOverallPanel.Rd | 11 ++--
man/mfaEstimate.Rd | 3 +-
man/phenoEstimate.Rd | 3 +-
man/scDDEstimate.Rd | 40 ++++++++++----
man/scDDSimulate.Rd | 10 +++-
man/setParam.Rd | 1 -
man/setParamUnchecked.Rd | 1 -
man/setParams.Rd | 1 -
man/simpleEstimate.Rd | 3 +-
man/sparseDCEstimate.Rd | 27 +++++++---
man/splatEstimate.Rd | 5 +-
man/splatSimulate.Rd | 21 ++++++--
man/splateQTL.Rd | 94 +++++++++++++++++++++++++++++++++
man/splateQTLGeneMeans.Rd | 22 ++++++++
man/splateQTLMeansMatrix.Rd | 25 +++++++++
man/splateQTLgenes.Rd | 19 +++++++
man/splateQTLnormMeansMatrix.Rd | 21 ++++++++
man/splateQTLpairs.Rd | 32 +++++++++++
man/splateQTLsnps.Rd | 22 ++++++++
man/splatter.Rd | 1 -
man/summariseStats.Rd | 3 +-
man/zinbEstimate.Rd | 52 +++++++++++++-----
37 files changed, 475 insertions(+), 98 deletions(-)
create mode 100644 man/splateQTL.Rd
create mode 100644 man/splateQTLGeneMeans.Rd
create mode 100644 man/splateQTLMeansMatrix.Rd
create mode 100644 man/splateQTLgenes.Rd
create mode 100644 man/splateQTLnormMeansMatrix.Rd
create mode 100644 man/splateQTLpairs.Rd
create mode 100644 man/splateQTLsnps.Rd
diff --git a/.travis.yml b/.travis.yml
index 2ca7ef4..639f1ef 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,7 +19,8 @@ addons:
- libgsl-dev # dependency for gsl>copula>zinbwave
- libmagick++-dev # dependency for magick
r_check_args: "--no-vignettes"
-#install: skip
+
+install: skip
#install:
# - R -e 'install.packages("knitr")'
# - R -e 'install.packages("devtools")'
diff --git a/DESCRIPTION b/DESCRIPTION
index b797881..cfc39ed 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -70,7 +70,7 @@ biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,
Software, ImmunoOncology
URL: https://github.com/Oshlack/splatter
BugReports: https://github.com/Oshlack/splatter/issues
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
Encoding: UTF-8
VignetteBuilder: knitr
Language: en-GB
diff --git a/man/BASiCSEstimate.Rd b/man/BASiCSEstimate.Rd
index c06c7fb..42cc7f1 100644
--- a/man/BASiCSEstimate.Rd
+++ b/man/BASiCSEstimate.Rd
@@ -6,19 +6,47 @@
\alias{BASiCSEstimate.matrix}
\title{Estimate BASiCS simulation parameters}
\usage{
-BASiCSEstimate(counts, spike.info = NULL, batch = NULL, n = 20000,
- thin = 10, burn = 5000, regression = TRUE,
- params = newBASiCSParams(), verbose = TRUE, progress = TRUE, ...)
+BASiCSEstimate(
+ counts,
+ spike.info = NULL,
+ batch = NULL,
+ n = 20000,
+ thin = 10,
+ burn = 5000,
+ regression = TRUE,
+ params = newBASiCSParams(),
+ verbose = TRUE,
+ progress = TRUE,
+ ...
+)
-\method{BASiCSEstimate}{SingleCellExperiment}(counts, spike.info = NULL,
- batch = NULL, n = 20000, thin = 10, burn = 5000,
- regression = TRUE, params = newBASiCSParams(), verbose = TRUE,
- progress = TRUE, ...)
+\method{BASiCSEstimate}{SingleCellExperiment}(
+ counts,
+ spike.info = NULL,
+ batch = NULL,
+ n = 20000,
+ thin = 10,
+ burn = 5000,
+ regression = TRUE,
+ params = newBASiCSParams(),
+ verbose = TRUE,
+ progress = TRUE,
+ ...
+)
-\method{BASiCSEstimate}{matrix}(counts, spike.info = NULL,
- batch = NULL, n = 20000, thin = 10, burn = 5000,
- regression = TRUE, params = newBASiCSParams(), verbose = TRUE,
- progress = TRUE, ...)
+\method{BASiCSEstimate}{matrix}(
+ counts,
+ spike.info = NULL,
+ batch = NULL,
+ n = 20000,
+ thin = 10,
+ burn = 5000,
+ regression = TRUE,
+ params = newBASiCSParams(),
+ verbose = TRUE,
+ progress = TRUE,
+ ...
+)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
diff --git a/man/addFeatureStats.Rd b/man/addFeatureStats.Rd
index 2ac4f6e..07b60e6 100644
--- a/man/addFeatureStats.Rd
+++ b/man/addFeatureStats.Rd
@@ -4,8 +4,13 @@
\alias{addFeatureStats}
\title{Add feature statistics}
\usage{
-addFeatureStats(sce, value = c("counts", "cpm", "tpm", "fpkm"),
- log = FALSE, offset = 1, no.zeros = FALSE)
+addFeatureStats(
+ sce,
+ value = c("counts", "cpm", "tpm", "fpkm"),
+ log = FALSE,
+ offset = 1,
+ no.zeros = FALSE
+)
}
\arguments{
\item{sce}{SingleCellExperiment to add feature statistics to.}
diff --git a/man/addGeneLengths.Rd b/man/addGeneLengths.Rd
index 057dac7..afb6e86 100644
--- a/man/addGeneLengths.Rd
+++ b/man/addGeneLengths.Rd
@@ -4,8 +4,13 @@
\alias{addGeneLengths}
\title{Add gene lengths}
\usage{
-addGeneLengths(sce, method = c("generate", "sample"), loc = 7.9,
- scale = 0.7, lengths = NULL)
+addGeneLengths(
+ sce,
+ method = c("generate", "sample"),
+ loc = 7.9,
+ scale = 0.7,
+ lengths = NULL
+)
}
\arguments{
\item{sce}{SingleCellExperiment to add gene lengths to.}
diff --git a/man/compareSCEs.Rd b/man/compareSCEs.Rd
index db1f4d7..cb6e247 100644
--- a/man/compareSCEs.Rd
+++ b/man/compareSCEs.Rd
@@ -4,8 +4,13 @@
\alias{compareSCEs}
\title{Compare SingleCellExperiment objects}
\usage{
-compareSCEs(sces, point.size = 0.1, point.alpha = 0.1, fits = TRUE,
- colours = NULL)
+compareSCEs(
+ sces,
+ point.size = 0.1,
+ point.alpha = 0.1,
+ fits = TRUE,
+ colours = NULL
+)
}
\arguments{
\item{sces}{named list of SingleCellExperiment objects to combine and
diff --git a/man/diffSCEs.Rd b/man/diffSCEs.Rd
index 97cb53b..de9cd40 100644
--- a/man/diffSCEs.Rd
+++ b/man/diffSCEs.Rd
@@ -4,8 +4,14 @@
\alias{diffSCEs}
\title{Diff SingleCellExperiment objects}
\usage{
-diffSCEs(sces, ref, point.size = 0.1, point.alpha = 0.1, fits = TRUE,
- colours = NULL)
+diffSCEs(
+ sces,
+ ref,
+ point.size = 0.1,
+ point.alpha = 0.1,
+ fits = TRUE,
+ colours = NULL
+)
}
\arguments{
\item{sces}{named list of SingleCellExperiment objects to combine and
diff --git a/man/expandParams.Rd b/man/expandParams.Rd
index c6f8379..58a0a52 100644
--- a/man/expandParams.Rd
+++ b/man/expandParams.Rd
@@ -1,7 +1,6 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/BASiCSParams-methods.R,
% R/LunParams-methods.R, R/SplatParams-methods.R
-\docType{methods}
\name{expandParams}
\alias{expandParams}
\alias{expandParams,BASiCSParams-method}
diff --git a/man/getParam.Rd b/man/getParam.Rd
index d73b728..2b01a81 100644
--- a/man/getParam.Rd
+++ b/man/getParam.Rd
@@ -1,6 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Params-methods.R
-\docType{methods}
\name{getParam}
\alias{getParam}
\alias{getParam,Params-method}
diff --git a/man/kersplatEstimate.Rd b/man/kersplatEstimate.Rd
index e73ebd9..d609070 100644
--- a/man/kersplatEstimate.Rd
+++ b/man/kersplatEstimate.Rd
@@ -8,11 +8,9 @@
\usage{
kersplatEstimate(counts, params = newKersplatParams(), verbose = TRUE)
-\method{kersplatEstimate}{SingleCellExperiment}(counts,
- params = newKersplatParams(), verbose = TRUE)
+\method{kersplatEstimate}{SingleCellExperiment}(counts, params = newKersplatParams(), verbose = TRUE)
-\method{kersplatEstimate}{matrix}(counts, params = newKersplatParams(),
- verbose = TRUE)
+\method{kersplatEstimate}{matrix}(counts, params = newKersplatParams(), verbose = TRUE)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
diff --git a/man/lun2Estimate.Rd b/man/lun2Estimate.Rd
index 956aa5a..1223b2f 100644
--- a/man/lun2Estimate.Rd
+++ b/man/lun2Estimate.Rd
@@ -6,15 +6,32 @@
\alias{lun2Estimate.matrix}
\title{Estimate Lun2 simulation parameters}
\usage{
-lun2Estimate(counts, plates, params = newLun2Params(), min.size = 200,
- verbose = TRUE, BPPARAM = SerialParam())
+lun2Estimate(
+ counts,
+ plates,
+ params = newLun2Params(),
+ min.size = 200,
+ verbose = TRUE,
+ BPPARAM = SerialParam()
+)
-\method{lun2Estimate}{SingleCellExperiment}(counts, plates,
- params = newLun2Params(), min.size = 200, verbose = TRUE,
- BPPARAM = SerialParam())
+\method{lun2Estimate}{SingleCellExperiment}(
+ counts,
+ plates,
+ params = newLun2Params(),
+ min.size = 200,
+ verbose = TRUE,
+ BPPARAM = SerialParam()
+)
-\method{lun2Estimate}{matrix}(counts, plates, params = newLun2Params(),
- min.size = 200, verbose = TRUE, BPPARAM = SerialParam())
+\method{lun2Estimate}{matrix}(
+ counts,
+ plates,
+ params = newLun2Params(),
+ min.size = 200,
+ verbose = TRUE,
+ BPPARAM = SerialParam()
+)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
diff --git a/man/lun2Simulate.Rd b/man/lun2Simulate.Rd
index 38c9ab3..b2e5082 100644
--- a/man/lun2Simulate.Rd
+++ b/man/lun2Simulate.Rd
@@ -4,8 +4,7 @@
\alias{lun2Simulate}
\title{Lun2 simulation}
\usage{
-lun2Simulate(params = newLun2Params(), zinb = FALSE, verbose = TRUE,
- ...)
+lun2Simulate(params = newLun2Params(), zinb = FALSE, verbose = TRUE, ...)
}
\arguments{
\item{params}{Lun2Params object containing simulation parameters.}
diff --git a/man/lunEstimate.Rd b/man/lunEstimate.Rd
index c313ad8..e257440 100644
--- a/man/lunEstimate.Rd
+++ b/man/lunEstimate.Rd
@@ -8,8 +8,7 @@
\usage{
lunEstimate(counts, params = newLunParams())
-\method{lunEstimate}{SingleCellExperiment}(counts,
- params = newLunParams())
+\method{lunEstimate}{SingleCellExperiment}(counts, params = newLunParams())
\method{lunEstimate}{matrix}(counts, params = newLunParams())
}
diff --git a/man/makeCompPanel.Rd b/man/makeCompPanel.Rd
index d9ec714..7120f8d 100644
--- a/man/makeCompPanel.Rd
+++ b/man/makeCompPanel.Rd
@@ -4,9 +4,12 @@
\alias{makeCompPanel}
\title{Make comparison panel}
\usage{
-makeCompPanel(comp, title = "Comparison", labels = c("Means",
- "Variance", "Mean-variance relationship", "Library size",
- "Zeros per gene", "Zeros per cell", "Mean-zeros relationship"))
+makeCompPanel(
+ comp,
+ title = "Comparison",
+ labels = c("Means", "Variance", "Mean-variance relationship", "Library size",
+ "Zeros per gene", "Zeros per cell", "Mean-zeros relationship")
+)
}
\arguments{
\item{comp}{list returned by \code{\link{compareSCEs}}.}
diff --git a/man/makeDiffPanel.Rd b/man/makeDiffPanel.Rd
index 4d772fe..3132c16 100644
--- a/man/makeDiffPanel.Rd
+++ b/man/makeDiffPanel.Rd
@@ -4,10 +4,12 @@
\alias{makeDiffPanel}
\title{Make difference panel}
\usage{
-makeDiffPanel(diff, title = "Difference comparison",
- labels = c("Means", "Variance", "Library size", "Zeros per cell",
- "Zeros per gene", "Mean-variance relationship",
- "Mean-zeros relationship"))
+makeDiffPanel(
+ diff,
+ title = "Difference comparison",
+ labels = c("Means", "Variance", "Library size", "Zeros per cell", "Zeros per gene",
+ "Mean-variance relationship", "Mean-zeros relationship")
+)
}
\arguments{
\item{diff}{list returned by \code{\link{diffSCEs}}.}
diff --git a/man/makeOverallPanel.Rd b/man/makeOverallPanel.Rd
index 4a0af66..07f2922 100644
--- a/man/makeOverallPanel.Rd
+++ b/man/makeOverallPanel.Rd
@@ -4,10 +4,13 @@
\alias{makeOverallPanel}
\title{Make overall panel}
\usage{
-makeOverallPanel(comp, diff, title = "Overall comparison",
- row.labels = c("Means", "Variance", "Mean-variance relationship",
- "Library size", "Zeros per cell", "Zeros per gene",
- "Mean-zeros relationship"))
+makeOverallPanel(
+ comp,
+ diff,
+ title = "Overall comparison",
+ row.labels = c("Means", "Variance", "Mean-variance relationship", "Library size",
+ "Zeros per cell", "Zeros per gene", "Mean-zeros relationship")
+)
}
\arguments{
\item{comp}{list returned by \code{\link{compareSCEs}}.}
diff --git a/man/mfaEstimate.Rd b/man/mfaEstimate.Rd
index 58a14f7..2b27927 100644
--- a/man/mfaEstimate.Rd
+++ b/man/mfaEstimate.Rd
@@ -8,8 +8,7 @@
\usage{
mfaEstimate(counts, params = newMFAParams())
-\method{mfaEstimate}{SingleCellExperiment}(counts,
- params = newMFAParams())
+\method{mfaEstimate}{SingleCellExperiment}(counts, params = newMFAParams())
\method{mfaEstimate}{matrix}(counts, params = newMFAParams())
}
diff --git a/man/phenoEstimate.Rd b/man/phenoEstimate.Rd
index ede4080..545bb09 100644
--- a/man/phenoEstimate.Rd
+++ b/man/phenoEstimate.Rd
@@ -8,8 +8,7 @@
\usage{
phenoEstimate(counts, params = newPhenoParams())
-\method{phenoEstimate}{SingleCellExperiment}(counts,
- params = newPhenoParams())
+\method{phenoEstimate}{SingleCellExperiment}(counts, params = newPhenoParams())
\method{phenoEstimate}{matrix}(counts, params = newPhenoParams())
}
diff --git a/man/scDDEstimate.Rd b/man/scDDEstimate.Rd
index 75bc1af..05c647c 100644
--- a/man/scDDEstimate.Rd
+++ b/man/scDDEstimate.Rd
@@ -7,18 +7,40 @@
\alias{scDDEstimate.default}
\title{Estimate scDD simulation parameters}
\usage{
-scDDEstimate(counts, params = newSCDDParams(), verbose = TRUE,
- BPPARAM = SerialParam(), ...)
+scDDEstimate(
+ counts,
+ params = newSCDDParams(),
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ ...
+)
-\method{scDDEstimate}{matrix}(counts, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam(), conditions, ...)
+\method{scDDEstimate}{matrix}(
+ counts,
+ params = newSCDDParams(),
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ conditions,
+ ...
+)
-\method{scDDEstimate}{SingleCellExperiment}(counts,
- params = newSCDDParams(), verbose = TRUE, BPPARAM = SerialParam(),
- condition = "condition", ...)
+\method{scDDEstimate}{SingleCellExperiment}(
+ counts,
+ params = newSCDDParams(),
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ condition = "condition",
+ ...
+)
-\method{scDDEstimate}{default}(counts, params = newSCDDParams(),
- verbose = TRUE, BPPARAM = SerialParam(), condition, ...)
+\method{scDDEstimate}{default}(
+ counts,
+ params = newSCDDParams(),
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ condition,
+ ...
+)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
diff --git a/man/scDDSimulate.Rd b/man/scDDSimulate.Rd
index 73916f3..ebe03e3 100644
--- a/man/scDDSimulate.Rd
+++ b/man/scDDSimulate.Rd
@@ -4,8 +4,14 @@
\alias{scDDSimulate}
\title{scDD simulation}
\usage{
-scDDSimulate(params = newSCDDParams(), plots = FALSE,
- plot.file = NULL, verbose = TRUE, BPPARAM = SerialParam(), ...)
+scDDSimulate(
+ params = newSCDDParams(),
+ plots = FALSE,
+ plot.file = NULL,
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ ...
+)
}
\arguments{
\item{params}{SCDDParams object containing simulation parameters.}
diff --git a/man/setParam.Rd b/man/setParam.Rd
index 7f8e4ea..e7dca4c 100644
--- a/man/setParam.Rd
+++ b/man/setParam.Rd
@@ -3,7 +3,6 @@
% R/KersplatParams-methods.R, R/Lun2Params-methods.R, R/LunParams-methods.R,
% R/Params-methods.R, R/PhenoParams-methods.R, R/SCDDParams-methods.R,
% R/SplatParams-methods.R, R/ZINBParams-methods.R
-\docType{methods}
\name{setParam}
\alias{setParam}
\alias{setParam,BASiCSParams-method}
diff --git a/man/setParamUnchecked.Rd b/man/setParamUnchecked.Rd
index 9ebd482..588f669 100644
--- a/man/setParamUnchecked.Rd
+++ b/man/setParamUnchecked.Rd
@@ -1,6 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/Params-methods.R
-\docType{methods}
\name{setParamUnchecked}
\alias{setParamUnchecked}
\alias{setParamUnchecked,Params-method}
diff --git a/man/setParams.Rd b/man/setParams.Rd
index 0e62af2..18756d3 100644
--- a/man/setParams.Rd
+++ b/man/setParams.Rd
@@ -1,7 +1,6 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/AllGenerics.R, R/KersplatParams-methods.R,
% R/Params-methods.R, R/SplatParams-methods.R
-\docType{methods}
\name{setParams}
\alias{setParams}
\alias{setParams,KersplatParams-method}
diff --git a/man/simpleEstimate.Rd b/man/simpleEstimate.Rd
index d764e1e..49cd2da 100644
--- a/man/simpleEstimate.Rd
+++ b/man/simpleEstimate.Rd
@@ -8,8 +8,7 @@
\usage{
simpleEstimate(counts, params = newSimpleParams())
-\method{simpleEstimate}{SingleCellExperiment}(counts,
- params = newSimpleParams())
+\method{simpleEstimate}{SingleCellExperiment}(counts, params = newSimpleParams())
\method{simpleEstimate}{matrix}(counts, params = newSimpleParams())
}
diff --git a/man/sparseDCEstimate.Rd b/man/sparseDCEstimate.Rd
index ba3d010..7d970d3 100644
--- a/man/sparseDCEstimate.Rd
+++ b/man/sparseDCEstimate.Rd
@@ -6,14 +6,29 @@
\alias{sparseDCEstimate.matrix}
\title{Estimate SparseDC simulation parameters}
\usage{
-sparseDCEstimate(counts, conditions, nclusters, norm = TRUE,
- params = newSparseDCParams())
+sparseDCEstimate(
+ counts,
+ conditions,
+ nclusters,
+ norm = TRUE,
+ params = newSparseDCParams()
+)
-\method{sparseDCEstimate}{SingleCellExperiment}(counts, conditions,
- nclusters, norm = TRUE, params = newSparseDCParams())
+\method{sparseDCEstimate}{SingleCellExperiment}(
+ counts,
+ conditions,
+ nclusters,
+ norm = TRUE,
+ params = newSparseDCParams()
+)
-\method{sparseDCEstimate}{matrix}(counts, conditions, nclusters,
- norm = TRUE, params = newSparseDCParams())
+\method{sparseDCEstimate}{matrix}(
+ counts,
+ conditions,
+ nclusters,
+ norm = TRUE,
+ params = newSparseDCParams()
+)
}
\arguments{
\item{counts}{either a counts matrix or an SingleCellExperiment object
diff --git a/man/splatEstimate.Rd b/man/splatEstimate.Rd
index d028711..a08e14d 100644
--- a/man/splatEstimate.Rd
+++ b/man/splatEstimate.Rd
@@ -8,8 +8,7 @@
\usage{
splatEstimate(counts, params = newSplatParams())
-\method{splatEstimate}{SingleCellExperiment}(counts,
- params = newSplatParams())
+\method{splatEstimate}{SingleCellExperiment}(counts, params = newSplatParams())
\method{splatEstimate}{matrix}(counts, params = newSplatParams())
}
@@ -25,7 +24,7 @@ SplatParams object containing the estimated parameters.
\description{
Estimate simulation parameters for the Splat simulation from a real
dataset. See the individual estimation functions for more details on how this
-is done.
+is done. I'm testing stuff now.
}
\examples{
# Load example data
diff --git a/man/splatSimulate.Rd b/man/splatSimulate.Rd
index 578477f..b0fcdfe 100644
--- a/man/splatSimulate.Rd
+++ b/man/splatSimulate.Rd
@@ -7,8 +7,13 @@
\alias{splatSimulatePaths}
\title{Splat simulation}
\usage{
-splatSimulate(params = newSplatParams(), method = c("single", "groups",
- "paths"), verbose = TRUE, ...)
+splatSimulate(
+ params = newSplatParams(),
+ method = c("single", "groups", "paths", "eqtl"),
+ eqtl = NaN,
+ verbose = TRUE,
+ ...
+)
splatSimulateSingle(params = newSplatParams(), verbose = TRUE, ...)
@@ -22,8 +27,13 @@ See \code{\link{SplatParams}} for details.}
\item{method}{which simulation method to use. Options are "single" which
produces a single population, "groups" which produces distinct groups
-(eg. cell types) or "paths" which selects cells from continuous
-trajectories (eg. differentiation processes).}
+(eg. cell types), "paths" which selects cells from continuous
+trajectories (eg. differentiation processes), or "eqtl" which produces
+a single population for every sample (ie column) in the dataframe
+output by splateQTL().}
+
+\item{eqtl}{matrix of mean gene counts across the eQTL population, output
+from splateQTL().}
\item{verbose}{logical. Whether to print progress messages.}
@@ -128,6 +138,9 @@ sim <- splatSimulate(params, mean.rate = 0.6, out.prob = 0.2)
sim <- splatSimulate(method = "groups")
# Simulate paths
sim <- splatSimulate(method = "paths")
+# Simulate eQTL data
+eqtl <- splateQTL(params=params)
+sim <- splatSimulate(params=params, method = 'eqtl', eqtl = eqtl)
}
}
\references{
diff --git a/man/splateQTL.Rd b/man/splateQTL.Rd
new file mode 100644
index 0000000..8d22408
--- /dev/null
+++ b/man/splateQTL.Rd
@@ -0,0 +1,94 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splat-eqtl.R
+\name{splateQTL}
+\alias{splateQTL}
+\title{Splat-eQTL}
+\usage{
+splateQTL(
+ params = newSplatParams(),
+ gff_file = "test_data/test.gff3",
+ snp_file = "test_data/test.vcf",
+ eqtlES_shape = 2.740558,
+ eqtlES_rate = 6.441281,
+ esnp.n = 100,
+ eqtl.dist = 1e+06,
+ eqtl.maf = 0.1,
+ eqtl.mafd = 0.01,
+ eqtl.bcv = 0.4,
+ eqtl.save = TRUE,
+ ...
+)
+}
+\arguments{
+\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{snp_file}{Path to real/simulated genotype data in .vcf format.
+Where each column is a sample and each row is a SNP.}
+
+\item{eqtlES_shape}{Effect Size shape parameter (default estimated from
+GTEx thyroid cis-eQTL data)}
+
+\item{eqtlES_rate}{Effect Size rate parameter (default estimated from
+GTEx thyroid cis-eQTL data)}
+
+\item{esnp.n}{Number of eSNP-eQTL associations to include}
+
+\item{eqtl.dist}{Distance between eSNP and eGene (TSS).}
+
+\item{eqtl.maf}{Desired Minor Allele Frequency (MAF) of eSNPs to include}
+
+\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
+\code{params}.}
+}
+\value{
+GeneMeansPop Matrix containing the simulated mean gene expression
+value for each gene (row) and each sample in the population (column).
+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.
+}
+\details{
+Parameters can be set in a variety of ways. If no parameters are provided
+the default parameters are used. Any parameters in \code{params} can be
+overridden by supplying additional arguments through a call to
+\code{\link{setParams}}. This design allows the user flexibility in
+how they supply parameters and allows small adjustments without creating a
+new \code{SplatParams} object. See examples for a demonstration of how this
+can be used.
+
+The eQTL Gene Mean simulation involves the following steps:
+\enumerate{
+ \item Load and format gene (GFF/GTF) and SNP (genotype) data.
+ \item Select eGenes-eSNPs pairs and assign effect sizes.
+ \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)
+}
+}
+\examples{
+# Load example data
+library(scater)
+set.seed(1)
+sce <- mockSCE()
+params <- splatEstimate(sce)
+pop.gMeans <- splateQTL(params)
+
+}
+\seealso{
+\code{\link{splateQTLgenes}}, \code{\link{splateQTLsnps}},
+\code{\link{splateQTLpairs}}, \code{\link{splateQTLnormMeansMatrix}},
+\code{\link{splateQTLGeneMeans}}, \code{\link{splateQTLMeansMatrix}}
+}
diff --git a/man/splateQTLGeneMeans.Rd b/man/splateQTLGeneMeans.Rd
new file mode 100644
index 0000000..e3ce7ec
--- /dev/null
+++ b/man/splateQTLGeneMeans.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splat-eqtl.R
+\name{splateQTLGeneMeans}
+\alias{splateQTLGeneMeans}
+\title{Set a gene mean expression value (not normalized) for each gene.}
+\usage{
+splateQTLGeneMeans(params, pairs, eqtl.bcv)
+}
+\arguments{
+\item{params}{Output from splateQTL_DefineAssociations}
+
+\item{pairs}{A dataframe eSNPs-eGenes pair assignments and their effect sizes}
+}
+\value{
+the eSNP-eGene pairs dataframe updated to include the mean gene
+expression level, BCV, and standard deviation.
+}
+\description{
+Assign a mean expression value to each gene, sampled from a gamma
+distribution parameterized by splatEstimate, then calculate the BCV and
+the standard deviation
+}
diff --git a/man/splateQTLMeansMatrix.Rd b/man/splateQTLMeansMatrix.Rd
new file mode 100644
index 0000000..dbb5d59
--- /dev/null
+++ b/man/splateQTLMeansMatrix.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splat-eqtl.R
+\name{splateQTLMeansMatrix}
+\alias{splateQTLMeansMatrix}
+\title{Un-normalize the mean gene expression matrix}
+\usage{
+splateQTLMeansMatrix(pairs, nMeans)
+}
+\arguments{
+\item{nMeans}{The normalized gene expression means for the population}
+
+\item{params}{A dataframe eSNPs-eGenes pair assignments and their effect sizes}
+}
+\value{
+MeansMatrix: Matrix of simulated gene means for eQTL population.
+}
+\description{
+Un-normalize the 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.
+}
diff --git a/man/splateQTLgenes.Rd b/man/splateQTLgenes.Rd
new file mode 100644
index 0000000..34a94bc
--- /dev/null
+++ b/man/splateQTLgenes.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splat-eqtl.R
+\name{splateQTLgenes}
+\alias{splateQTLgenes}
+\title{Process gene data}
+\usage{
+splateQTLgenes(gff_file)
+}
+\arguments{
+\item{gff_file}{Path to GFF/GTF file}
+}
+\value{
+A dataframe containing gene IDs and locations.
+}
+\description{
+Read in GFF/GTF file (ignorning 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).
+}
diff --git a/man/splateQTLnormMeansMatrix.Rd b/man/splateQTLnormMeansMatrix.Rd
new file mode 100644
index 0000000..01970e6
--- /dev/null
+++ b/man/splateQTLnormMeansMatrix.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splat-eqtl.R
+\name{splateQTLnormMeansMatrix}
+\alias{splateQTLnormMeansMatrix}
+\title{Generate normalized mean gene expression matrix for whole eQTL population}
+\usage{
+splateQTLnormMeansMatrix(snps, pairs)
+}
+\arguments{
+\item{snps}{The dataframe with the genetic marker info}
+
+\item{pairs}{A dataframe eSNPs-eGenes pair assignments and their effect sizes}
+}
+\value{
+normGeneMeansPop: matrix of normalized mean gene exp. levels.
+}
+\description{
+Use the approach outlined in Huang et. al 2018 (NAR) to assign normalized
+mean expression levels for each gene for each sample. Where:
+y = Effect Size * genotype + error, where error ~ Norm(0,1)
+}
diff --git a/man/splateQTLpairs.Rd b/man/splateQTLpairs.Rd
new file mode 100644
index 0000000..72dbec5
--- /dev/null
+++ b/man/splateQTLpairs.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splat-eqtl.R
+\name{splateQTLpairs}
+\alias{splateQTLpairs}
+\title{Select eGenes-eSNPs pairs and assign effect sizes.}
+\usage{
+splateQTLpairs(genes, snps, esnp.n, eqtl.dist, eqtlES_shape, eqtlES_rate)
+}
+\arguments{
+\item{genes}{Dataframe with gene ID and location}
+
+\item{snps}{Dataframe with SNP ID, location, and sample genotypes}
+
+\item{esnp.n}{Number of eSNP-eQTL associations to include}
+
+\item{eqtl.dist}{Distance between eSNP and eGene (TSS).}
+
+\item{eqtlES_shape}{Effect Size shape parameter (default estimated from
+GTEx thyroid cis-eQTL data)}
+
+\item{eqtlES_rate}{Effect Size rate parameter (default estimated from
+GTEx thyroid cis-eQTL data)}
+}
+\value{
+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
+using the GTEx data from the thyroid tissue.
+}
diff --git a/man/splateQTLsnps.Rd b/man/splateQTLsnps.Rd
new file mode 100644
index 0000000..3f914a3
--- /dev/null
+++ b/man/splateQTLsnps.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/splat-eqtl.R
+\name{splateQTLsnps}
+\alias{splateQTLsnps}
+\title{Process genotype data}
+\usage{
+splateQTLsnps(snp_file, eqtl.maf, eqtl.mafd)
+}
+\arguments{
+\item{snp_file}{Path to real/simulated genotype data in .ped.gen format}
+
+\item{eqtl.maf}{Desired Minor Allele Frequency (MAF) of eSNPs to include}
+
+\item{eqtl.mafd}{Maximum variation from eqtl.maf to include as eSNP}
+}
+\value{
+A dataframe containing SNP names, locations, and sample genotypes.
+}
+\description{
+Read in SNP (genotype matrix) file and remove extra columns. Then calculate
+the Minor Allele Frequency and filter SNPs outside of the MAF range defined.
+}
diff --git a/man/splatter.Rd b/man/splatter.Rd
index fcb0392..52e5aa0 100644
--- a/man/splatter.Rd
+++ b/man/splatter.Rd
@@ -3,7 +3,6 @@
\docType{package}
\name{splatter}
\alias{splatter}
-\alias{splatter-package}
\title{splatter.}
\description{
\pkg{splatter} is a package for the well-documented and reproducible
diff --git a/man/summariseStats.Rd b/man/summariseStats.Rd
index 72459e4..1e53f97 100644
--- a/man/summariseStats.Rd
+++ b/man/summariseStats.Rd
@@ -4,8 +4,7 @@
\alias{summariseStats}
\title{Summarise statistics}
\usage{
-summariseStats(data, split.col, stat.cols, measure = c("MAD", "MAE",
- "RMSE"))
+summariseStats(data, split.col, stat.cols, measure = c("MAD", "MAE", "RMSE"))
}
\arguments{
\item{data}{The data.frame to summarise}
diff --git a/man/zinbEstimate.Rd b/man/zinbEstimate.Rd
index 11bece2..ae32dc9 100644
--- a/man/zinbEstimate.Rd
+++ b/man/zinbEstimate.Rd
@@ -6,21 +6,47 @@
\alias{zinbEstimate.matrix}
\title{Estimate ZINB-WaVE simulation parameters}
\usage{
-zinbEstimate(counts, design.samples = NULL, design.genes = NULL,
- common.disp = TRUE, iter.init = 2, iter.opt = 25,
- stop.opt = 1e-04, params = newZINBParams(), verbose = TRUE,
- BPPARAM = SerialParam(), ...)
+zinbEstimate(
+ counts,
+ design.samples = NULL,
+ design.genes = NULL,
+ common.disp = TRUE,
+ iter.init = 2,
+ iter.opt = 25,
+ stop.opt = 1e-04,
+ params = newZINBParams(),
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ ...
+)
-\method{zinbEstimate}{SingleCellExperiment}(counts,
- design.samples = NULL, design.genes = NULL, common.disp = TRUE,
- iter.init = 2, iter.opt = 25, stop.opt = 1e-04,
- params = newZINBParams(), verbose = TRUE, BPPARAM = SerialParam(),
- ...)
+\method{zinbEstimate}{SingleCellExperiment}(
+ counts,
+ design.samples = NULL,
+ design.genes = NULL,
+ common.disp = TRUE,
+ iter.init = 2,
+ iter.opt = 25,
+ stop.opt = 1e-04,
+ params = newZINBParams(),
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ ...
+)
-\method{zinbEstimate}{matrix}(counts, design.samples = NULL,
- design.genes = NULL, common.disp = TRUE, iter.init = 2,
- iter.opt = 25, stop.opt = 1e-04, params = newZINBParams(),
- verbose = TRUE, BPPARAM = SerialParam(), ...)
+\method{zinbEstimate}{matrix}(
+ counts,
+ design.samples = NULL,
+ design.genes = NULL,
+ common.disp = TRUE,
+ iter.init = 2,
+ iter.opt = 25,
+ stop.opt = 1e-04,
+ params = newZINBParams(),
+ verbose = TRUE,
+ BPPARAM = SerialParam(),
+ ...
+)
}
\arguments{
\item{counts}{either a counts matrix or a SingleCellExperiment object
--
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