fluximplied: fluximplied

In sportiellomike/fluximplied: Pathway analysis software utilizing rate limiting steps

fluximplied

Description

Pathway analysis of DESeq2 result or character vector of differentially expressed genes which also plots results.

Usage

fluximplied(
  inputdat,
  species = "mmu",
  geneformat = "SYMBOL",
  padjcolname = "adj_pvalue",
  inputformat = "df",
  LFCcolname = "log2FoldChange",
  pcutoff = 0.05
)

Arguments

inputdat	what you are using as your input data, either a data frame with genes as the rownames, a column for LFC, and a column for padj values
species	either mus or hsa
geneformat	either ENTREZ or symbol
padjcolname	the name of the column in your data frame, if applicable, that stores the padj values
inputformat	either df or vector
LFCcolname	the name of the column in your data frame, if applicable, that stores the Log2FoldChange Values
pcutoff	the alpha threshold for your padjustadjust

Value

If a data frame was supplied, it should also return a data frame as well as a bar graph of the enriched pathways.

Examples

fluximplied(inputdat = exampleData,
geneformat="SYMBOL",
species = "mmu",
padjcolname = 'padj',
inputformat = 'df',
LFCcolname = 'log2FoldChange',
pcutoff = 0.05)

sportiellomike/fluximplied documentation built on Jan. 30, 2024, 12:46 p.m.