csSamWrapper function - performs entire functionality

Share:

Description

csSamWrapper function - performs entire functionality

Usage

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")

Arguments

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)

Value

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.

Author(s)

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

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

See Also

csfit,csSAM,fdrCsSAM,plotCsSAM