DEseq2_export: Prepares DESeq2 object for visualization

In Rvirgenslane/Hotgenes: For Visualizing Differential Expression Analysis

Prepares DESeq2 object for visualization

Description

Prepares DESeq2 object for visualization

Usage

DEseq2_export(
  DEseq2_object = NULL,
  lfcShrink_type = "normal",
  resultsSel = NULL,
  rlog_export = TRUE,
  padj_cut = 0.1,
  ...
)

Arguments

DEseq2_object	the output object generated by DESeq2
lfcShrink_type	"normal" (Default) is the original DESeq2 shrinkage estimator. Other options is "apeglm".
resultsSel	values from DESeq2 resultsNames function. If NULL (default) DE for all results will be reported.
rlog_export	Logical value, if TRUE (default), data normalized by rlog will be exported. If FALSE, only varianceStabilizingTransformation normalization will be used.
padj_cut	the adjusted pvalue cut off for differential expression. Default = 0.1
...	additional parameters for lfcShrink function

Value

list of R objects needed for Shiny_DE_viz function

See Also

lfcShrink

Examples

dds_con_dir<-system.file("extdata",
"dds_con.Rdata", package = "Hotgenes", mustWork = TRUE)
load(dds_con_dir)
library(DESeq2)
resultsNames(dds_con)
Example_Hotgenes<-DEseq2_export(DEseq2_object = dds_con, 
resultsSel = contrast_selec<-c("shEWS","Hrs2","Hrs6",
"shEWS.Hrs2","shEWS.Hrs6"), padj_cut = 0.1)
Example_Hotgenes$Exported_plots$transformation_plots
Example_Hotgenes$Exported_plots$boxplot_rlog
Example_Hotgenes$Exported_plots$boxplot_vsd

Rvirgenslane/Hotgenes documentation built on June 15, 2024, 2:16 a.m.