MetaQC: Meta QC main function to calculate score table and SMR value

In metaOmic/MetaQC: Objective quality control and inclusion/ exclusion criteria for genomic meta-analysis

Usage

MetaQC(DList = NULL, colLabel = NULL, GList = NULL, filterGenes = FALSE, 
  cutRatioByMean = 0.3, cutRatioByVar = 0.3, pvalCutGene = 0.05, 
  pvalAdjustGene = TRUE, pvalCutPath = 0.05, pvalAdjustPath = TRUE, 
  minNumGenes = 5, maxNumGenes = 200, B = 100)

Arguments

DList	a list of study matrix
colLabel	a list of column label for each study
GList	a list for gene sets (pathway)
filterGenes	a bool variable to filter genes or not
cutRatioByMean	if filterGenes==TRUE, the percentage of filtering genes by low mean value
cutRatioByVar	if filterGenes==TRUE, the percentage of filtering genes by low variance value
pvalCutGene	p-value cutoff for gene to decide significant DE genes
pvalAdjustGene	a bool variable to adjust gene p-value or not
pvalCutPath	p-value cutoff for gene set enrichment analysis to decide significant pathway
pvalAdjustPath	a bool variable to adjust pathway p-value or not
minNumGenes	minimum number of genes inside a pathway
maxNumGenes	maximum number of genes inside a pathway
B	permutation times for EQC

Value

scoreTable	scoreTable for each measurement
SMR	SMR value for each study

Author(s)

Silvia Liu <[e-mail]>

References

Kang, Dongwan D., et al. MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. Nucleic acids research 40.2 (2012): e15-e15.

metaOmic/MetaQC documentation built on May 22, 2019, 6:54 p.m.