fdrCsSAM0: fdrCsSAM - Deprecated Version

Description Usage Arguments Value Note Author(s) References

Description

Estimates the false discovery rate for the identified cell-specific differences in gene expression.

Usage

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fdrCsSAM0(G, cc, y, n, numcell, numgene, rhat, nperms,
  alternative = c("two.sided", "greater", "less"), standardize = TRUE,
  medianCenter = TRUE, logRm = FALSE, logBase = 2, nonNeg = FALSE)

Arguments

G

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

n

A nuermic vector describing the number of samples in a group

numcell

The number of cell-types to consider

numgene

The number of genes being considered

rhat

The contrast in cell-type expression for each cell-type as observed between the two groups being compared.

nperms

The number of permutations to perform.

alternative

Type of test to conduct - choose between 'two.sided','greater',or 'less'

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.

Value

A list.

fdr.g

A matirx false dicovery rates for csSAM comparison for each cell-type at different thresholds. A set of 100 theresholds is determined automatically from the data (k by 100, where k is number of cells).

avrhatperm
rhatperm

A matrix sized pXkXg which stores the contrast of a given gene g in cell type k in permutation p of the data.

cutp.g

A matrix k by 100, where k is the number of cell tpes. Lists the 100 cutoff thresholds for each cell-type as determined automatically from the computed contrast.

rhat

A matrix object with the result of contrasting 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).

ncall.g

Number of genes called significant at the given cutoff threshold with a FDR matching that indicated in fdr.g

Note

From version 1.3, the FDR computation is implemented in C++, using Rcpp.

Author(s)

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

C++ implementation/optimisation by Renaud Gaujoux.

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.