run_select_contrasts: Shiny gadget to upload groups and select contrasts

In crossmeta: Cross Platform Meta-Analysis of Microarray Data

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)

crossmeta documentation built on Nov. 8, 2020, 8 p.m.