intersect_significant: Find the sets of intersecting significant genes

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Find the sets of intersecting significant genes

Description

Use extract_significant_genes() to find the points of agreement between limma/deseq/edger.

Usage

intersect_significant(
  combined,
  lfc = 1,
  p = 0.05,
  padding_rows = 2,
  z = NULL,
  p_type = "adj",
  selectors = c("limma", "deseq", "edger"),
  order = "inverse",
  excel = "excel/intersect_significant.xlsx",
  ...
)

Arguments

combined	Result from combine_de_tables().
lfc	Define significant via fold-change.
p	Or p-value.
padding_rows	How much space to put between groups of data?
z	Use a z-score filter?
p_type	Use normal or adjusted p-values.
selectors	List of methods to intersect.
order	When set to the default 'inverse', go from the set with the most least intersection to the most. E.g. Start with abc,bc,ac,c,ab,b,a as opposed to a,b,ab,c,ac,bc,abc.
excel	An optional excel workbook to which to write.
...	Extra arguments for extract_significant_genes() and friends.

Value

List containing the intersections between the various DE methods for both the up and down sets of genes. It should also provide some venn diagrams showing the degree of similarity between the methods.

Examples

 ## Not run: 
  expt <- create_expt(metadata="some_metadata.xlsx", gene_info=funkytown)
  big_result <- all_pairwise(expt, model_batch=FALSE)
  pretty <- combine_de_tables(big_result, excel="excel/combined_expt.xlsx")
  intersect <- intersect_significant(pretty, excel="excel/intersecting_genes.xlsx")
 
## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.