gene_browser: Launch a browser of DE analysis results
In bihealth/bioshmods: What the Package Does (One Line, Title Case)

gene_browser

R Documentation

Launch a browser of DE analysis results

Description

Launch a simple shiny-based browser of DE analysis results

Usage

gene_browser(
  x,
  annot_linkout = NULL,
  cols_to_hide = c("stat", "lfcSE", "symbol", "entrez"),
  primary_id = "PrimaryID"
)

Arguments

`x`	object holding the DE analysis results. List containing the elements `contrasts`, `covariates`, `expression` and `annotation`.
`annot_linkout`	a list; see Details.
`cols_to_hide`	columns in the contrasts data frames to hide in the table. Default is for DESeq2 derived contrasts.
`primary_id`	The name of the column in `contrasts` and `annotation` which holds the primary, unique identifier of genes.

Details

Creates a shiny app, which allows to show gene expression profiles.

Value

does not return a value

Examples

if(interactive()) {
  data(C19)
  annot_linkout <- list(
    SYMBOL="https://www.genecards.org/cgi-bin/carddisp.pl?gene=%s",
    ENTREZ="https://www.ncbi.nlm.nih.gov/gene/?term=%s"
  )
  gene_browser(C19, annot_linkout=annot_linkout)
}

bihealth/bioshmods documentation built on July 1, 2023, 4:32 a.m.