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Run Differential Expression Wrapper

Source: R/diffexp_functions.R
run_diffexp_wrapper.Rd

This function runs the differential expression analysis and generates MA and volcano plots for a single comparison

Usage

run_diffexp_wrapper(
  dds,
  org,
  group_by,
  comparison,
  order = "pxfc",
  save_dir = getwd()
)

Arguments

dds

DESeq2 object containing the expression data

org

The organism to use, either "human" or "mouse".

group_by

Column name in colData(dds) to use for grouping.

comparison

Comparison to run.

order

Column name to use for ranking genes. Default is "pxfc"

save_dir

Directory where all output files will be saved. Default is current working directory

one_to_all

Logical. If TRUE, runs one-to-all comparisons. Default is FALSE

Value

A data frame containing differential expression results for a comparison

Examples

if (FALSE) { # \dontrun{
# Run differential expression pipeline
res <- run_diffexp_wrapper(dds)

# Run with custom grouping
res <- run_diffexp_wrapper(dds, group_by = "Treatment")
} # }