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Get expression values

Source: R/gene_plot.R
get_expr_values.Rd

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
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.integer()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
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
#> Warning: Direct call of 'as.data.frame.factor()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
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