meta_analysis: Function to perform meta analysis for HIPC ImmuneSignatures...
In ehfhcrc/ImmSigPkg: Run HIPC ImmuneSignatures Pipeline from ImmuneSpace data

Function to perform meta analysis for HIPC ImmuneSignatures Project

1
2
3

meta_analysis(geneSetDB, rds_data_dir, cohort, FDR.cutoff = 0.5,
  pvalue.cutoff = 0.01, endPoint = "fc_res_max_d30", adjusted = F,
  baselineOnly = T, indiv_rds = F, markdown = F, output_dir)

`geneSetDB`	table defining gene sets
`rds_data_dir`	Directory holding eset objects as rds files
`cohort`	Study cohort, young or old
`FDR.cutoff`	Cutoff for q-values in selecting significant gene sets
`pvalue.cutoff`	cutoff for p-values in selecting significant gene sets
`endPoint`	HAI table column used for categorizing response
`adjusted`	Use age-adjusted gene expression values, default = FALSE
`baselineOnly`	Use only day zero gene expression values, default = TRUE
`indiv_rds`	Output individual rds files for each discovery study, default = FALSE
`markdown`	Set output to go directly to screen for markdown files, default = FALSE
`output_dir`	Output directory