analysis_deps_anova: Differential expression analysis using ANOVA

In ecnuzdd/PhosMap: A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

Differential expression analysis using ANOVA

Description

Differential expression analysis using ANOVA

Usage

analysis_deps_anova(
  expr_data_frame,
  group,
  log2_label = FALSE,
  return_padjust = TRUE,
  adjust_method = "BH"
)

Arguments

expr_data_frame	A data frame containing ID and quantification values.
group	A factor representing experimental groups.
log2_label	A boolean value for representing whether the value is logarithmic or not, the default is FALSE.
return_padjust	A boolean value for representing whether or not the p value is adjusted, the default is TRUE.
adjust_method	Method used to adjust the p-values for multiple testing. See p.adjust for the complete list of options, the default is "BH".

Value

A data frame containing ID, log2(FC) and p value.

Author(s)

Dongdong Zhan and Mengsha Tong

Examples

## The process needs to load data from PhosMap datasets stored into FTP server and perform large computation.
## It may take a few minutes.
if(FALSE){
ftp_url <- "ftp://111.198.139.72:4000/pub/PhosMap_datasets/function_demo_data/analysis_deps_anova.RData"
load_data <- load_data_with_ftp(ftp_url, 'RData')
writeBin(load_data, "analysis_deps_anova.RData")
load("analysis_deps_anova.RData")

anova_result <- analysis_deps_anova(
  expr_data_frame, group, log2_label = FALSE,
  return_padjust = TRUE, adjust_method = 'BH'
)
head(anova_result)

}

ecnuzdd/PhosMap documentation built on Dec. 7, 2022, 4:09 a.m.