Get expression values

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

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)
#> using counts and average transcript lengths from tximeta
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)
#> using 'avgTxLength' from assays(dds), correcting for library size

df_exp <- get_expression_values(dds_macrophage,
  gene = "ENSG00000125347",
  intgroup = "condition"
)
head(df_exp)
#>                 exp_value   condition
#> SAMEA103885102   819.6422       naive
#> SAMEA103885347 31852.1503        IFNg
#> SAMEA103885043 17874.4499      SL1344
#> SAMEA103885392 71361.7711 IFNg_SL1344
#> SAMEA103885182  1239.2723       naive
#> SAMEA103885136 41985.4038        IFNg