Description Usage Arguments Value Methods (by class)
View source: R/csSAMfit.R View source: R/csSAMfit.R
Fits a csSAM Model
1 2 3 4 5 6 7 8 9 10 11  csSAMfit(x, ...)
## S3 method for class 'formula'
csSAMfit(x, data = NULL, ...)
## Default S3 method:
csSAMfit(x, cc, y = NULL, covariates = NULL,
nperms = 200, alternative = c("all", "two.sided", "greater", "less"),
fit = c("auto", "block", "lm", "monovariate"), standardize = TRUE,
medianCenter = TRUE, logRm = FALSE, logBase = 2, nonNeg = NULL,
keep.all = FALSE, verbose = FALSE, .rng = NULL, ...)

x 
target matrix assayed on mixed samples. 
... 
arguments passed down to the relevant S3 method. 
cc 
Matrix of cellfrequency. (n by k, n samples, k celltypes) 
y 
A numeric vector of group association of each sample. Either 1 or 2. 
covariates 
matrix of covariates to include in the model, e.g., for correcting for gender, age or batch effects. 
nperms 
The number of permutations to perform. 
alternative 
two.sided less greater 
fit 
fitting method, that dictates the type of model that is fitted:

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 cellspecific expression estimated as negative, to a ceiling of 0. It is conservative in its study of differential expression. Default is TRUE. 
keep.all 
logical that indicates if the statistics of all the permutations should be also
returned in slot 
verbose 
single logical or integer that controls verbosity levels. 
.rng 
specification of the initial RNG settings, that are set using rngtools::setRNG. 
a csSAMfit
object, that is a list with the following elements:
*
*
*
formula
: convenient formula interface that can take advantage of expression and
sample annotation data stored in Biobase::ExpressionSet objects.
default
: workhorse method that takes model elements in separate
arguments.
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