\HeaderA{gsealmPerm}{Nonparametric inference for linear models in Gene-Set-Enrichment
Analysis (GSEA)}{gsealmPerm}
\keyword{methods}{gsealmPerm}
\begin{Description}\relax
Provides permutation-based p-values for a main effect at the gene-set
level, potentially adjusting for the effect of other variables via a
linear model. This is a generalization and upgrade of \code{\LinkA{gseattperm}{gseattperm}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
gsealmPerm(eSet, formula = "", mat, nperm, na.rm = TRUE,...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{eSet}] An \code{ExpressionSet} object.
\item[\code{formula}] An object of class \code{\LinkA{formula}{formula}} (or one that can be coerced to
that class), specifying only the right-hand side starting with
the '~' symbol. The LHS is automatically set as the expression
levels provided in  \code{eSet}. The names of all predictors must
exist in the phenotypic data of \code{eSet}. See more below in "Details".
\item[\code{mat}] A 0/1 incidence matrix with each row representing a gene set
and each column representing a gene.  A 1 indicates membership of a gene in a gene set. 
\item[\code{nperm}] Number of permutations used to simulate the reference
null distribution.
\item[\code{na.rm}] Should missing observations be ignored? 
\item[\code{...}] Additional parameters passed on to \code{\LinkA{GSNormalize}{GSNormalize}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
If a formula is provided, the permutation test permutes sample (i.e. column) labels, so
essentially the effect is compared with the null distribution of
effects for *each particular gene-set separately*. This neutralizes the impact of
intra-sample correlations.
If the formula contains two or more covariates, the effect of interest
must be the first one in the formula. This effect's covariate values are permuted within each subgroup defined by identical values
on all other covariates. This means, that the other
covariates *must* be discrete, otherwise the analysis is meaningless. The effect of interest is the only one that 
can be continuous.

If a formula is *not* provided, a row-permutation test is performed on average expression levels. This test examines 
whether each gene-set is differentially expressed (on the average), compared with a permutation baseline of 
random gene-sets of the same size.
\end{Details}
\begin{Value}
A matrix with the same number of rows as 'mat' and two columns,
"Lower" and "Upper".  The "Lower" ("Upper") column gives
the probability of seeing a t-statistic smaller (larger) than the
observed. If 'mat' had row names, so will the output.
\end{Value}
\begin{Section}{Warnings}
1. Inference is *only* for the first term in the
model. If you want inference for more terms, re-run the function on the
same model, changing order of terms each time.

2. To repeat: the adjusting covariates (all terms except the first) have to be discrete. Adding a continuous
covariate with unique values for most samples, may result in an infinite
loop. However, you *can* put a continuous covariate as your first term.
\end{Section}
\begin{Note}\relax
This function is a generic template for GSEA permutation tests. The
particular type of GSEA statistic 
used is determined by \code{\LinkA{GSNormalize}{GSNormalize}}, which is called by this function.
\end{Note}
\begin{Author}\relax
Assaf Oron
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{gseattperm}{gseattperm}},\code{\LinkA{GSNormalize}{GSNormalize}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(sample.ExpressionSet)

### Generating random pseudo-gene-sets
fauxGS=matrix(sample(c(0,1),size=50000,replace=TRUE,prob=c(.9,.1)),nrow=100)

### inference for sex: sex is first term
sexPvals=gsealmPerm(sample.ExpressionSet,~sex+type,mat=fauxGS,nperm=40)

### inference for type: type is first term
typePvals=gsealmPerm(sample.ExpressionSet,~type+sex,mat=fauxGS,nperm=40,removeShift=TRUE)

### plotting the p-values; note that the effect direction depends upon
### factor level order (defaults to alphabetical)
layout(t(1:2))
### Sex p-values are center-heavy, typical when the effect is dominated
### by another effect
hist(sexPvals[,2],10,main="Sex Effect p-values",xlab="p-values for Male minus Female",xlim=c(0,1))
### The dominating effect is type, where there is a baseline shift in
### favor of controls
hist(typePvals[,1],10,main="Type Effect p-values",xlab="p-values for Case minus Control",xlim=c(0,1))

############
### Modeling type again - and now we add a baseline-shift removal (the 'removeShift' argument passed on to 'GSNormalize')
typePvals1=gsealmPerm(sample.ExpressionSet,~type+sex,mat=fauxGS,nperm=40,removeShift=TRUE)
### Modeling type again - and now the shift removal is by mean instead
### of the default median
typePvals2=gsealmPerm(sample.ExpressionSet,~type+sex,mat=fauxGS,nperm=40,removeShift=TRUE,removeStat=mean)

### Now notice the differences between the 3 versions! This is a weird
### dataset indeed; it's also important to undrestand which research
### question you are trying to answer :)
hist(typePvals1[,1],10,main="Type Effect p-values",xlab="p-values for Case minus Control",xlim=c(0,1))
hist(typePvals2[,1],10,main="Type Effect p-values",xlab="p-values for Case minus Control",xlim=c(0,1))

\end{ExampleCode}
\end{Examples}

