csSAMfit: Fits a csSAM Model
In shenorrLab/csSAM: csSAM - cell-specific Significance Analysis of Microarrays

Description Usage Arguments Value Methods (by class)

Fits a csSAM Model

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 cell-frequency. (n by k, n samples, k cell-types)
`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: auto: automatic selection based on input data and model specification (e.g., presence of covariates) block: two linear models are fitted within each group of samples. Only works when the variable of interest is a factor (categorical variable). lm: full interaction linear model. monovariate: model is fitted including one cell type at a time. This could be a work around for when there are many more cell types than samples in a given group.
`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 TRUE.
`keep.all`	logical that indicates if the statistics of all the permutations should be also returned in slot `rhatperm`.
`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.

shenorrLab/csSAM documentation built on May 29, 2019, 9:23 p.m.