cum_freq_data: A data formating function for inverse-cummulative DEG...

In MetaVolcanoR: Gene Expression Meta-analysis Visualization Tool

Description

This function counts how many genes consistly appears as DE along the input studies

Usage

cum_freq_data(meta_diffexp, nstud)

Arguments

meta_diffexp	data.frame/data.table containing all the input studies
nstud	the number of inputed GEO2R outputs <integer>

Value

data.frame inverse cummulative distribution

Examples

library(dplyr)
data(diffexplist)
diffexp <- lapply(diffexplist, function(...) deg_def(..., "pvalue", 
           "Log2FC", 0.05, 0))
diffexp <- rename_col(diffexp, "Symbol")
meta_diffexp <- Reduce(function(...) merge(..., by = "Symbol", all = TRUE),
           diffexp)
meta_diffexp %>%
dplyr::select(dplyr::matches("deg_")) %>%
    data.matrix -> n_deg
meta_diffexp[['ndeg']] <- rowSums(n_deg^2, na.rm = TRUE)
cfd <- cum_freq_data(meta_diffexp, length(diffexplist))
head(cfd, 3)

MetaVolcanoR documentation built on Nov. 8, 2020, 7:52 p.m.