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.
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, , .