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Return QC plots

get_dge_qc_plot.Rd

Getter function to extract the QC plots from the BulkDge() class. These are added when you run for example qc_bulk_dge() and normalise_bulk_dge(). You can either leave the plot choice as NULL and provide input when prompted, or you provide the name. The possible plots that might be in the class

  • p1_nb_genes_cohort Proportion of non-zero genes for the samples in the respective cohorts (added after using qc_bulk_dge()).

  • p2_outliers An outlier plot based on the data from p1, added after using qc_bulk_dge().

  • p3_voom_normalization Initial Voom normalisation plot after filtering lowly expressed genes. Added after using normalise_bulk_dge().

  • p4_boxplot_normalization Expression levels after normalisation. Added after using normalise_bulk_dge().

  • p5_pca_case_control A PCA plot with the chosen case control category. Added if calculate_pca_bulk_dge() is run.

  • p6_batch_correction_plot A PCA plot pre and post batch correction with the case-control category overlayed. Added if batch_correction_bulk_dge() is run.

Usage

get_dge_qc_plot(object, plot_choice = NULL)

Arguments

object

BulkDge class.

plot_choice

Optional string or integer. Index or name of the plate.

Value

Returns the DGEList stored in the class.

Examples

# pull a named QC plot back off the object
syn <- synthetic_bulk_cor_matrix()
meta <- data.table::data.table(
  sample_id = colnames(syn$counts),
  case_control = rep(c("case", "control"), each = 50)
)
object <- BulkDge(raw_counts = syn$counts, meta_data = meta)
object <- qc_bulk_dge(object, group_col = "case_control", .verbose = FALSE)
get_dge_qc_plot(object, plot_choice = "p1_nb_genes_cohort")