get_expression_values {GeneTonic} | R Documentation |
Extract expression values, with the possibility to select other assay slots
get_expression_values(dds, gene, intgroup, assay = "counts", normalized = TRUE)
dds |
A |
gene |
Character, specifies the identifier of the feature (gene) to be extracted |
intgroup |
A character vector of names in |
assay |
Character, specifies with assay of the |
normalized |
Logical value, whether the expression values should be
normalized by their size factor. Defaults to TRUE, applies when |
A tidy data.frame with the expression values and covariates for further processing
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)