run_select_contrasts {crossmeta} | R Documentation

## Shiny gadget to upload groups and select contrasts

### Description

Shiny gadget to upload groups and select contrasts

### Usage

    run_select_contrasts(
      eset,
      gse_name,
      prev = NULL,
      app_dir = system.file("select_contrasts", package = "crossmeta", mustWork = TRUE),
      port = 3838
    )

### Arguments

`eset` | ExpressionSet
`gse_name` | GEO accession for the series.
`prev` | Previous result of `diff_expr`. Used to allow rechecking previous selections.
`app_dir` | Directory to shiny app. For local development use 'inst/select_contrasts'. Default is in 'select_contrasts' sub directory of crossmeta package.

### Value

result of setup_prev. Used to specify sample groups and contrasts for differential expression analysis.

library(lydata) # location of data data_dir <- system.file("extdata", package = "lydata")

# gather GSE names gse_name <- "GSE9601"

# load previous analysis eset <- load_raw(gse_name, data_dir)[[1]] run_select_contrasts(eset, gse_name)

[Package crossmeta version 1.16.1 Index]