Get expression values — get_expr

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

Usage

get_expr_values(
  de_container,
  gene,
  intgroup,
  assay = "counts",
  normalized = TRUE
)

Arguments

de_container: An object containing the data for a Differential Expression workflow (e.g. DESeq2, edgeR or limma). Currently, this can be 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(de_container) to use for grouping.
assay: Character, specifies with assay of the de_container 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"

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)
keep <- rowSums(counts(dds_macrophage) >= 10) >= 6
dds_macrophage <- dds_macrophage[keep, ]
# dds_macrophage <- DESeq(dds_macrophage)

df_exp <- get_expr_values(
  de_container = dds_macrophage,
  gene = "ENSG00000125347",
  intgroup = "condition"
)
#> using 'avgTxLength' from assays(dds), correcting for library size
head(df_exp)
#>                 exp_value   condition
#> SAMEA103885102   819.3101       naive
#> SAMEA103885347 31872.5798        IFNg
#> SAMEA103885043 17931.2679      SL1344
#> SAMEA103885392 71740.9927 IFNg_SL1344
#> SAMEA103885182  1230.1864       naive
#> SAMEA103885136 41761.1942        IFNg