VERSION 1.0.0
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Initial release of package BLMA includes:
* bilevelAnalysisGeneset: a function to perform a bi-level meta-analysis in conjunction with geneset enrichment methods (ORA/GSA/PADOG) to integrate multiple gene expression datasets.
* bilevelAnalysisPathway: a function to perform a bi-level meta-analysis conjunction with Impact Analysis to integrate multiple gene expression datasets.
* intraAnalysisClassic: a function to perform an intra-experiment analysis in conjunction with any of the classical hypothesis testing methods, such as t-test, Wilcoxon test, etc.
* bilevelAnalysisClassic: a function to perform a bi-level meta-analysis in conjunction with any of the classical hypothesis testing methods, such as t-test, Wilcoxon test, etc.
* intraAnalysisGene: a function to 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
* bilevelAnalysisGene: a function to perform a bi-level meta-analysis in conjunction with the moderate t-test (limma package) for the purpose of differential expression analysis of multiple gene expression datasets
* loadKEGGPathways: this function loads KEGG pathways and names
* addCLT: a function to combine independent studies using the average of p-values
* fisherMethod: a function to combine independent p-values using the minus log product
* stoufferMethod: a function to combine independent studies using the sum of p-values transformed into standard normal variables