fdrSAM: fdrSAM

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

Description

Calculate the false discovery rate (FDR) by permutation for the group differences as calculated by SAM.

Usage

fdrSAM(G, y, nperms, tt.sam, alternative = "two.sided")

Arguments

G	Matrix of gene expression, columns ordered in the same order at the cell-frequency matrix (n by g, n samples, g genes)
y	A numeric vector of group association of each sample. Either 1 or 2.
nperms	Number of permutations to run. User responsability to the number appropriately fitting the sample size.
tt.sam	Real group comparison t-test statistic value
alternative	Type of test. Choices are 'two.sided','greater' or 'less'

Value

A list

fdr.sam	A vector false dicovery rates for SAM comparison at different thresholds. A set of 100 theresholds is determined automatically from the data.
ncall.sam	Number of genes called significant at the given cutoff threshold with a FDR matching that indicated in fdr.sam
ttstar.sam	A matrix listing the t statistic for each gene in each permutation. (p by g, p permutations, g genes)
sigGene.sam	A vector of length equal to the number of genes being considered. For each gene the estimated FDR is listed.

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, 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.