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

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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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:

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

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