csSAM: csSAM

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

Description

Computes the constrast between groups for the deconvolved cell-specific expression for each cell-type

Usage

csSAM(ghat1, se1, n1, ghat2, se2, n2, standardize, medianCenter = TRUE,
  nonNeg = FALSE, stat.only = TRUE)

Arguments

ghat1	Expression matrix of deconvolved cell-specific gene expression estimates for group 1.
se1	Standard error group 1
n1	Group 1 size
ghat2	Expression matrix of deconvolved cell-specific gene expression estimates for group 2.
se2	Standard error group 2
n2	Group 2 size
standardize	Standardize contrast values, into SAM shrinked statistic.
medianCenter	Median center rhat distributions for each cell-type
nonNeg	Negative values not allowed such as in a single channel microarray. Zero them if negative (a conervative option)
stat.only	logical that indicates if the returned object should consists in the matrix of cell type-specific SAM statistic only, or contain more detailed data about the fit (see section Value).

Value

A matrix object that contains the – standardised – contrast of the average cell-specific expression profile of the two groups, per cell-type (Size k by g where k is the number of cells and g is the number of genes).

If stat.only=FALSE, then result is a list with the following elements, where matrix elements have cell types in rows and genes in columns:

coefficients

a matrix of cell-specific contrasts between the two groups

se

a matrix of cell-specific standard errors

s0

a matrix of cell-specific standard error SAM shrinkage

stat

a matrix of – possibly median-centered – cell-specific SAM shrinked t-test statistics

stat.med

a vector containing the medians of each cell-specific SAM shrinked t-test statistics

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.