sigidentDEG: Perform DEG Analysis in Gene Expression Datasets Derived from...

In miracum/clearly-sigident.func: Sigident Functional Analysis

Perform DEG Analysis in Gene Expression Datasets Derived from MicroArrays

Description

One function to perform DEG analysis.

Usage

sigidentDEG(
  mergeset,
  mergedset,
  sample_metadata,
  diagnosis,
  idtype,
  fdr,
  plotdir = "./plots/",
  csvdir = "./tables/"
)

Arguments

mergeset	A matrix of merged expression sets (rows = genes, columns = samples). The output of the funtion 'sigident.preproc::load_geo_data()'.
mergedset	A large merged Expression Data set. The output of the funtion 'sigident.preproc::load_geo_data()'.
sample_metadata	A data frame. The data frame holding the sample metadata.
diagnosis	A vector of integers, holding the binary outcome variable (0 = "Control", 1 = "Target").
idtype	A character string. The type of ID used to name the genes. One of 'entrez' or 'affy' intended to use either entrez IDs or affy IDs. Caution: when using entrez IDs, missing and duplicated IDs are being removed!
fdr	A positive numeric value between (max. 0.05) indicating the desired q-Value during DEG analysis (Default: 0.01).
plotdir	A character string. Path to the folder to store resulting plots. Default: "./plots/".
csvdir	A character string. Path to the folder to store output tables. Default: "./tables/".

miracum/clearly-sigident.func documentation built on June 28, 2022, 3:16 p.m.