findSigGene: findSigGene
In shenorrLab/csSAM: csSAM - cell-specific Significance Analysis of Microarrays

Description Usage Arguments Value Note Author(s) References

Find the false discovery rate for each gene in each cell-type.

1 2	findSigGene(rhat, csSAMData, alternative = c("two.sided", "less", "greater"), version = getOption("csSAM.siggene.version", 2))

`rhat`	Matrix of cell-specific contrasts for each gene in each cell-type as computed for the original group classification.
`csSAMData`	List object returned from fdrCsSAM.
`alternative`	alternative hypothesis being tested: `'two.sided'`, `'less'` or `'greater'`
`version`	number that indicates the version of computation to perform: 1 or 2. Current default is `version = 2`, which fixes an issue for alternatives `'less'` and `'greater'`. Use `version = 1` to obtain old behaviour.

A matrix size k by g where k is the number of cell-types and g is the number of genes. For each cell in the matirx, listed is the FDR of the gene for a difference in a given cell-type.

From version 1.3, the FDR computation is implemented in C++, using Rcpp.

Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang

C++ implementation/optimisation by Renaud Gaujoux

Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ (2010). “Cell type-specific gene expression differences in complex tissues.” Nature methods, 7(4), pp. 287-9. ISSN 1548-7105, doi: 10.1038/nmeth.1439 (URL: http://doi.org/10.1038/nmeth.1439).

shenorrLab/csSAM documentation built on May 29, 2019, 9:23 p.m.