get_expression_values {GeneTonic} | R Documentation

## 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)

[Package GeneTonic version 1.6.4 Index]