volcano_plot: Title Volcano plot

In nkurniansyah/Olivia: RNA-seq Analysis

Title Volcano plot

Description

Title Volcano plot

Usage

volcano_plot(deg_res, significant_threshold)

Arguments

deg_res	A data frame of results differential of expression genes
significant_threshold	threshold for significant genes based on empirical-padj bh, example: 0.1

Value

volcano plot

Examples

library(ggrepel)
library(dplyr)
data(rnaseq_count_matrix)
rnaseq_count_matrix<- rnaseq_count_matrix[rowSums(rnaseq_count_matrix)>0,]
data(phenotype)
trait<-"Trait.1"
covars<-"Age+Sex"

median_norm<- median_normalization(rnaseq_count_matrix)
clean_count_matrix <- apply_filters(count_matrix = median_norm, median_min = 1, expression_sum_min = 10, 
                                   max_min = 10, range_min = 5, prop_zero_max = 0.5)
deg_res<-lm_count_mat_emp_pval(count_matrix=clean_count_matrix, pheno=phenotype, trait=trait, covariates_string=covars, 
                             n_permute=100, log_transform = "log_replace_half_min",
                             seed = NULL,outcome_type="continuous")
volcano_plot(deg_res=deg_res,significant_threshold=0.1 )

nkurniansyah/Olivia documentation built on July 29, 2023, 9:10 a.m.