plotCsSAM: plotcsSAM

In csSAM: csSAM - cell-specific Significance Analysis of Microarrays

Description

Plots the # of genes called significnat at a given false disocvery rate for the SAM (heterogenous tissue) comparison, and for each of the contrasted cell-types using csSAM

Usage

  plotCsSAM(csSAMdata, SAMdata, alternative, cellID,
    numcell, fileName)

Arguments

csSAMdata	List object output of the fdrCsSAM function
SAMdata	List object output of the fdrSAM function
alternative	Type of test conducted. Will appear in plot title.
cellID	Label for each cell-type
numcell	Number of different cell-types being considered.
fileName	Name of output pdf file.

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>.

csSAM documentation built on May 2, 2019, 5:52 a.m.