Usage
csSamWrapper(G, cc, y, nperms = 200, alternative = "two.sided", standardize = TRUE, medianCenter = TRUE, logRm = FALSE, logBase = 2, nonNeg = TRUE, fileName = "csSAMout.pdf")
Arguments
G
Matrix of gene expression, columns ordered in
the same order at the cell-frequency matrix (n by g, n
samples, g 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.
nperms
The number of permutations to perform.
alternative
two.sided less greater
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.
fileName
PDF file containing plots of FDR vs.
number of genes called for whole tissue comparison (via
SAM) as well as each cell-type (by csSAM)