get_expression_values: Get expression values

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Get expression values

Description

Extract expression values, with the possibility to select other assay slots

Usage

get_expression_values(
  dds,
  gene,
  intgroup,
  assay = "counts",
  normalized = TRUE,
  gtl = NULL
)

Arguments

dds	A DESeqDataSet object, normally obtained after running your data through the DESeq2 framework.
gene	Character, specifies the identifier of the feature (gene) to be extracted
intgroup	A character vector of names in colData(dds) to use for grouping.
assay	Character, specifies with assay of the dds object to use for reading out the expression values. Defaults to "counts".
normalized	Logical value, whether the expression values should be normalized by their size factor. Defaults to TRUE, applies when assay is "counts"
gtl	A GeneTonic-list object, containing in its slots the arguments specified above: dds, res_de, res_enrich, and annotation_obj - the names of the list must be specified following the content they are expecting

Value

A tidy data.frame with the expression values and covariates for further processing

Examples

library("macrophage")
library("DESeq2")
library("org.Hs.eg.db")
library("AnnotationDbi")

# dds object
data("gse", package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)

df_exp <- get_expression_values(dds_macrophage,
  gene = "ENSG00000125347",
  intgroup = "condition"
)
head(df_exp)

federicomarini/GeneTonic documentation built on Dec. 21, 2024, 10:05 p.m.