CellMix 1.6

Cell-specific Differential Expression with csSAM

Description

This function is adapted from the function csSamWrapper in the csSAM package, to integrate the csSAM algorithm from Shen-Orr et al. (2010) into the CellMix framework of deconvolution algorithms.

Usage

.csSAM(Y, x, data = NULL, nperms = 200, alternative = c("all", "two.sided", "greater", 
  "less"), standardize = TRUE, medianCenter = TRUE, logRm = FALSE, logBase = 2, 
      nonNeg = TRUE, verbose = lverbose())

Arguments

Y
target global gene expression matrix (n x p), with samples in columns, ordered in the same order at the cell proportions data in x.
x
known cell proportions as a matrix (k x p) or an NMF-class model containing the cell proportions in the coefficient matrix -- and a normally empty basis matrix. The proportions must be ordered in the same order as the samples in the target matrix. For csTopTable, a csSAM fit as return by ged.
data
specification of the sample groups. If not missing, it must be a factor or coercible to a factor, with length the number of samples, i.e. columns, in the target matrix.
nperms
The number of permutations to perform. It is only used when computing cell-specific differential expression between groups specified in argument data.
verbose
logical that indicates if verbose messages should be shown.
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.

Value

Returns an NMF model object, with the cell specific differential expression stored in the basis matrix.

The following details about the fit can be extracted using basisfit: csfitA list object containing a fit (cell-type specific differential expression) for each sample group. Each element in the list is an object returned by csfit. csSAMfit A list output of the fdrCsSAM function, containing data from the FDR computation. These are used by the csplot and csTopTable methods associated with csSAM fits.

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, , .

See also

csfit,csSAM,fdrCsSAM

Author

Original function: Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang Adaptation for CellMix: Renaud Gaujoux