Function reference • parcutils

get_star_align_log_summary(): Get alignment summary from the output of STAR program.

normalise_counts(): Convert raw read counts in to normalised values.

run_deseq_analysis(): Run differential expression (DE) analysis for several comparisosns at a time. Internally it uses DESeq2::DESeq() to perform DE analysis.

get_fold_change_matrix(): Prepare a fold change matrix

get_normalised_expression_matrix(): Prepare a matrix of normalised gene expression values.

get_genes_by_regulation() get_genesets_by_regulation(): Get genes based on their differential regulation

get_go_emap_plot(): Perform gene ontology analysis and visualization for DE genesets in one go.

save_go_data(): Save GO data in a excel file.

save_go_plots(): Save GO plot(s) in .pdf files.

gsea_analysis(): Perform GSEA using Molecular Signature Database (MSigDB).

enrichMsigDB(): Perform over representation analysis (ORA) against Molecular Signature Database (MsigDB) .

gseMsigDB(): Perform gene set enrichment analysis against Molecular Signature Database (MSigDB).

get_pairwise_corr_plot(): Get a scatter plot showing correlation between replicates.

get_corr_heatbox(): Generate a correlation heat plot.

get_gene_expression_box_plot(): Generate a box plot

get_gene_expression_heatmap() get_fold_change_heatmap(): Generate a heatmap of normalised gene expression values, z-score or log2Fold-change values.

get_heatmap_data(): Get data from a heatmap in the same order.

get_pca_plot(): Generate a PCA plot.

get_upset_intersects(): Get intersects of upset plot.

EnhancedVolcano2(): Wrapper around EnhancedVolcano::EnhancedVolcano()

get_volcano_plot(): Generate a volcano plot.

plot_deg_upsets(): Generate upset plots for differently expressed genes between comparisons.

plot_regions_relative_to_reference(): Generate segment plot to visualize genomic regions related to reference regions.

get_star_align_log_summary_plot(): Visualise alignment stats in a bar plot

get_diff_gene_count_barplot(): Generate a barplot of DEG counts.

get_gene_expression_line_plot() get_fold_change_line_plot(): Generate a line plot for gene expression / fold change values.

get_fold_change_scatter_plot(): Compare log2 fold change between two sample comparisons.

plot_deg_venn(): Generate a venn diagram showing overlap between DE genes.

Others

get_intergenic_signals(): Find signal intensity of intergenic regions.

named_group_split(): Split grouped data with names. A wrapper around dplyr::group_by() ref: https://github.com/tidyverse/dplyr/issues/4223

sort_geom_box(): Sort order of box obtained from geom_boxplot

ggsave2(): Wrapper around ggsave.

get_ASE_counts_barplot(): Generate a barplot showing counts of alternate splice events from the object NxtSe.

run_ase_diff_analysis(): Perform ASE diff analysis using edgeR.

get_diff_ASE_count_barplot(): Generate a barplot of diff ASE counts.

get_ASE_data_matrix(): Get a data matrix (PSI, logit, z-score) for a given ASE

get_ase_data_matrix_heatmap(): Generate a heatmap for a given list of ASE.

get_genes_from_event_name(): Get gene names from spliceWiz's EventName column.

event_region_to_granges(): Convert SpliceWiz's EventRegion column to GRanges object.

get_ASE_by_regulation() get_ASEsets_by_regulation(): Get Alternate Splice Events based on their differential regulation.

get_ase_volcano_plot(): Generate a volcano plot for diff. ASE.

event_region_to_coordinate(): Convert event regions to genomic co-ordinates.

get_event_annotations(): Annotate event names to event length, seq and GC.

plot_deASE_venn(): Plot a venn diagram for diff ASE (using event names or gene names) between multiple comparison.

make_parcutils_chip(): Construct a parcutils_chip object

normalised_matrix_to_rpm(): Convert normalised matrix into RPM signal

import_topn_bed_features(): Import top features (ranked by score) from a bed file.

make_enriched_heatmap_list(): Create a HeatmapList from parcutils_chip.

get_chip_signal_heatmap(): Generate a ChIP signal heatmap for a given sample. #' @description This function plots the ChIP signal heatmap for the given set of target region. ChIP signals shown in the plot will be plotted as an output of EnrichedHeatmap::normalizeToMatrix().

get_chip_signal_over_control_heatmap(): Generate a ChIP signal heatmap of treatment over control.

get_five_prime_flank_motif(): Get a seqlogo for flanking region across five prime end of the genomic range.

get_three_prime_flank_motif(): Get a seqlogo for flanking region across three prime end of the genomic range.

plot_chip_pairwise_correlation_heatmap(): Generate a pairwise correlation for chipseq data.