csSamWrapper: csSamWrapper function - performs entire functionality
In csSAM: csSAM - cell-specific Significance Analysis of Microarrays

Description Usage Arguments Value Author(s) References See Also

View source: R/csSamWrapper.R

csSamWrapper function - performs entire functionality

  csSamWrapper(G, cc, y, nperms = 200,
    alternative = "two.sided", standardize = TRUE,
    medianCenter = TRUE, logRm = FALSE, logBase = 2,
    nonNeg = TRUE, fileName = "csSAMout.pdf")

`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)

Returns a list containing:

`deconv`	A list object containing a fit (cell-type specfic expression) for each group. Each element in the list is an object returned by csFit.
`fdr.csSAM`	A list output of the fdrCsSAM function.
`fdr.SAM`	A list output of the fdrSAM function.
`sigGene.csSAM`	A list of significant genes.
`fileName`	The filename into whcih the FDR plots are dumped.

Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang

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, <URL: http://dx.doi.org/10.1038/nmeth.1439>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/20208531>.

csfit,csSAM,fdrCsSAM,plotCsSAM

csSAM documentation built on May 2, 2019, 5:21 p.m.