intraAnalysisGene: Intra-experiment analysis of an expression dataset at the...

In BLMA: BLMA: A package for bi-level meta-analysis

Description

perform an intra-experiment analysis in conjunction with the moderated t-test (limma package) for the purpose of differential expression analysis of a gene expression dataset

Usage

intraAnalysisGene(data, group, splitSize = 5, metaMethod = addCLT)

Arguments

data	a data frame where the rows are the gene IDs and the columns are the samples
group	sample grouping. The elements of group are either 'c' (control) or 'd' (disease). names(group) should be identical to colnames(data)
splitSize	the minimum number of disease samples in each split dataset. splitSize should be at least 3. By default, splitSize=5
metaMethod	the method used to combine p-values. This should be one of addCLT (additive method [1]), fishersMethod (Fisher's method [5]), stoufferMethod (Stouffer's method [6]), max (maxP method [7]), or min (minP method [8])

Details

This function performs an intra-experiment analysis [1] for individual genes of the given dataset. The function first splits the dataset into smaller datasets, performs a moderated t-test (limma package) for the genes of the split datasets, and then combines the p-values for individual genes using metaMethod

Value

A data frame (rownames are gene IDs) that consists of the following information:

• logFC: log foldchange (diseases versus controls)

• pLimma: p-value obtained from limma without spliting

• pLimma.fdr: FDR-corrected p-values of pLimma

• pIntra: p-value obtained from intra-experiment analysis

• pIntra.fdr: FDR-corrected p-values of pIntra

Author(s)

Tin Nguyen and Sorin Draghici

References

[1] T. Nguyen, R. Tagett, M. Donato, C. Mitrea, and S. Draghici. A novel bi-level meta-analysis approach – applied to biological pathway analysis. Bioinformatics, 32(3):409-416, 2016.

See Also

bilevelAnalysisGene, intraAnalysisClassic, link{bilevelAnalysisClassic}

Examples

data(GSE33223)
X <- intraAnalysisGene(data_GSE33223, group_GSE33223)
head(X)

BLMA documentation built on Nov. 8, 2020, 8:15 p.m.