Description Usage Arguments Value Author(s) References Examples

This function calculates the permutation gene set enrichment analysis test statistic and p-value without actually running the permutation. We account for the covariance among the genes within the set and approximate the corresponding permutation distribution. For more details on the method see Larson and Owen (2014).

1 |

`x` |
A matrix of expression data or an object of type ExpressionSet.
The columns of x represent samples in a given experiment. The rows are genes.
The names of each row (or |

`y` |
A vector containing the treatment for each sample. The length of y must be more than 4 for the "chisq" approximation. Each treatment group must have at least two observations for all approximation methods. There can only be two treatment groups. |

`covars` |
A vector or matrix containing covariate(s) of interest, optional |

`set` |
A |

`approx` |
A string of either "norm" (default), "beta" or "chiSq". If "norm", the normal approximation to the non-permutation GSEA is calculated and returned. If "beta", the beta approximation is reported. If "chiSq", the Chi-squared approximation to the permutation GSEA is calculated. |

`w` |
A vector or list containing the weights of each gene in the set or sets, optional. If w is a list, the number of elements in the list must correspond to the number of gene sets in the collection. |

`epsilonBetaAdj` |
A boolean indicating whether or to not to use an epsilon adjusted p-value for the Beta approximation. When TRUE, this prevents observed p-values of 0. The default is TRUE. |

`scaleXY` |
A boolean indicating whether or to not to scale x and y. The default is TRUE. |

`uniVarX` |
A boolean indicating whether or to not to scale x to have unit variance. The default is TRUE. |

An object with the corresponding GSEA results. If approx="norm" an `npGSEAResultNorm`

object is returned. If approx="beta" a `npGSEAResultBeta`

object is returned. If approx="chiSq"
a `npGSEAResultChiSq object`

is returned. If set is a `GeneSetCollection`

(i.e., multiple
sets of interest), then the corresponding `npGSEAResultNormCollection`

,
`npGSEAResultBetaCollection`

, or `npGSEAResultChiSqCollection`

is returned.

Jessica L. Larson and Art Owen

Jessica L Larson and Art B Owen: Moment based gene set tests. BMC Bioinformatics 2015, 16:132. http://www.biomedcentral.com/1471-2105/16/132

1 2 3 4 5 6 | ```
set.seed(15)
yFactor <- as.factor( c(rep("treated", 5), rep("control", 5)) )
xData <- matrix(data=rnorm(length(letters)*10) ,nrow=length(letters), ncol=10)
rownames(xData) <- letters
geneSetABC15 <- GeneSet(geneIds=letters[1:15], setName="setABC15")
res <- npGSEA(x = xData, y = yFactor, set = geneSetABC15)
``` |

```
Loading required package: GSEABase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
No methods found in package 'BiocGenerics' for request: 'unlist' when loading 'npGSEA'
```

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