csSAM (version 1.2.4)

findSigGene: findSigGene

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.

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, , .