runSAM

Description

A lightweight version of the SAM algorithm, only performs two group comparison with equal deltas on each tail

Usage

1
  runSAM(G, y, s0.sam = NULL, stand.r = TRUE)

Arguments

G

Matrix of gene expression, columns ordered in the same order at the cell-frequency matrix (n by p, n samples, p genes)

y

Numeric group association of each sample. Either 1 or 2.

s0.sam

Input or computed value of SAM exchangeability factor. Default is determined automatically

stand.r

Median center and standardize arrays. Default is TRUE.

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>.