canwefluxitup: canwefluxitup

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

canwefluxitup

Description

This function makes sure that your arguments are formatted correctly. You can call it, but it is also called within fluximplied().

Usage

canwefluxitup(
  inputdat = inputdat,
  species = species,
  geneformat = geneformat,
  padjcolname = padjcolname,
  LFCcolname = LFCcolname,
  pcutoff = pcutoff
)

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
LFCcolname	the name of the column in your data frame, if applicable, that stores the Log Fold Change values
pcutoff	the alpha threshold for your padjustadjust

Value

It should stop and print out what is wrong with your inputs if anything.

Examples

canwefluxitup(inputdat=exampleData,
species='mmu',
geneformat='SYMBOL',
padjcolname='adj_pvalue',
LFCcolname='Log2FoldChange',
pcutoff=0.05)

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