tr_clean_deseq2_result: Tidy results from DESeq2

In travis-m-blimkie/tRavis: tRavis: an R package by Travis Blimkie

Tidy results from DESeq2

Description

Helper function to filter and sort results from DESeq2, to aid in identifying differentially expressed genes.

Usage

tr_clean_deseq2_result(
  deseq2_result,
  p_adjusted = 0.05,
  fold_change = 1.5,
  inform = TRUE
)

Arguments

deseq2_result	Results object for DE genes, of class DESeqResults
p_adjusted	Threshold for adjusted p-value. Defaults to 0.05.
fold_change	Threshold for absolute fold change. Defaults to 1.5.
inform	Should a message be printed with the name of the DE comparison and number of DE genes found? Defaults to TRUE.

Value

A data frame (tibble) of filtered DE genes; see ?DESeq2::results for details on the output.

References

https://bioconductor.org/packages/DESeq2/

See Also

https://www.github.com/travis-m-blimkie/tRavis

Examples

ex_deseq_result <-
  readRDS(system.file("extdata", "ex_deseq_results.rds", package = "tRavis"))

tr_clean_deseq2_result(ex_deseq_result)

travis-m-blimkie/tRavis documentation built on April 9, 2024, 11:45 p.m.