Usage
fdrCsSAM(G, cc, y, n, numcell, numgene, rhat, nperms, alternative = "two.sided", standardize = TRUE, medianCenter = TRUE, logRm = FALSE, logBase = 2, nonNeg = FALSE)
Arguments
G
Matrix of gene expression, columns ordered in
the same order at the cell-frequency matrix (n by p, n
samples, p genes)
cc
Matrix of cell-frequency. (n by k, n samples, k
cell-types)
y
A numeric vector of group association of each
sample. Either 1 or 2.
n
A nuermic vector describing the number of
samples in a group
numcell
The number of cell-types to consider
numgene
The number of genes being considered
rhat
The contrast in cell-type expression for each
cell-type as observed between the two groups being
compared.
nperms
The number of permutations to perform.
alternative
Type of test to conduct - choose
between 'two.sided','greater',or 'less'
standardize
Standardize sample or not. Default is
TRUE
medianCenter
Median center rhat distributions.
Default is TRUE.
logRm
Exponentiate data for deconvolution stage.
Default is FALSE
logBase
Base of logaritm used to determine
exponentiation factor. Default is 2
nonNeg
For single channel arrays. Set any
cell-specific expression estimated as negative, to a
ceiling of 0. It is conservative in its study of
differential expression. Default is FALSE.