run_select_contrasts {crossmeta} | R Documentation |
Shiny gadget to upload groups and select contrasts
run_select_contrasts( eset, gse_name, prev = NULL, app_dir = system.file("select_contrasts", package = "crossmeta", mustWork = TRUE), port = 3838 )
eset |
ExpressionSet |
gse_name |
GEO accession for the series. |
prev |
Previous result of |
app_dir |
Directory to shiny app. For local development use 'inst/select_contrasts'. Default is in 'select_contrasts' sub directory of crossmeta package. |
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)