findSigGene: findSigGene

Description Usage Arguments Value Note Author(s) References

View source: R/findSigGene.R

Description

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

Usage

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

Arguments

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.

Value

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.

Note

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

Author(s)

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

C++ implementation/optimisation by Renaud Gaujoux

References

Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ (2010). <e2><80><9c>Cell type-specific gene expression differences in complex tissues.<e2><80><9d> 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 26, 2017, 8:06 a.m.