Description Usage Arguments Value Author(s) References See Also
csSamWrapper function - performs entire functionality
1 2 3 4 | 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
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