findSigGene: findSigGene

In csSAM: csSAM - cell-specific Significance Analysis of Microarrays

Description

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

Usage

  findSigGene(G, cc, y, rhat, csSAMData)

Arguments

G	Gene expression matrix of heterogenous tissue measurements
cc	Matrix of cell-frequency measures per person
y	Numeric group association of each sample. Either 1 or 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.

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.

Author(s)

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

References

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, <URL: http://dx.doi.org/10.1038/nmeth.1439>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/20208531>.

csSAM documentation built on May 2, 2019, 5:52 a.m.