plotCsSAM: plotcsSAM

In shenorrLab/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(csfit, sam, alternative = "two.sided", fileName, ..., height = 8,
  width = 10)

Arguments

csfit	csSAM fitted model as returned by csSAMfit.
sam	List object output of the fdrSAM function
alternative	Type of test conducted. Will appear in plot title.
fileName	Name of output pdf file.
...	other arguments passed to plot.csSAMfit.
height, width	output height and width

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, doi: 10.1038/nmeth.1439 (URL: http://doi.org/10.1038/nmeth.1439).

shenorrLab/csSAM documentation built on May 29, 2019, 9:23 p.m.