Function reference • DEP2

All functions

DEGdata-class: Class "DEGdata" This class store the test result from DESeq2

add_rejections(<SummarizedExperiment>) add_rejections(<DEGdata>): Mark significant proteins

GS_imp_wrapper(): pre_processing_GS_wrapper

ID_transform(): ID transform SE or DEGdata

NAiszero(): Transform NA to 0 in assay of a SummarizedExperiment

Order_cols(): Set order of experiment design for SummarizedExperiment

PPInetwork(): Draw a network on PPI result

Silicosis_ExpDesign: Silicosis_ExpDesign - experiment design of silicosis mouse proteome

Silicosis_peptide: Silicosis_peptide - peptide quantity data of a silicosis mouse model

Silicosis_pg: Silicosis_pg - proteinGroups data of a silicosis mouse model

Silicosis_phos: Silicosis_phos - phosphoproteome result of a silicosis mouse model

aggregate_pe(): Summarize peptide quantity to protein quantity

annoSpecies_df(): Species information table

check_PPI_depends(): Check required packages for PPI analysis.

check_RNAseq_depends(): Check required packages for DESeq2.

check_enrichment_depends(): Check required packages for enrichment analysis.

check_organismDB_depends(): Check organism annotation package

clean_character(): Clean characters in expression columns

correct_PTM_by_Protein(): correct_PTM_by_Protein

downloadAbsentFile(): Title

filter_pe(): Filter Qfeatures object on missing values or formula

filter_se(): Filter SummarizedExperiment on missing values or formula

get_ORA_result(): Extract significant enrichment terms base on giving threshold

get_contrast(): Get contrast(s) from SummarizedExperiment or DEGdata

get_df_long(): Generate a long data.frame from a SummarizedExperiment

get_df_wide(): Generate a wide data.frame from a SummarizedExperiment

get_exdesign_parse(): Construct experiment design basic on colnames parse

get_prefix(): Obtain the longest common prefix

get_results(): Generate a results table

get_signicant(): Extract significant candidates from SummarizedExperiment or DEGdata

get_suffix(): Obtain the longest common suffix

get_tc_cluster(): Time-course clustering

impute(): Impute missing values

impute_pe(): Impute a QFeatures object

load_PPIdata(): Check and load a local STRING data. If local file do not exist, will try to download from STRING.

make_dds(): Count matrix to DESeqDataSet conversion using an experimental design

make_dds_parse(): Count matrix to DESeqDataSet conversion by parsing from column names

make_pe(): Data.frame to QFeatures object conversion using an experimental design

make_pe_parse(): Data.frame to QFeatures object conversion by parsing column names

make_se(): Data.frame to SummarizedExperiment object conversion using an experimental design

make_se_parse(): Data.frame to SummarizedExperiment object conversion using parsing from column names

make_unique(): Make unique names

make_unique_ptm(): Make unique names for a modication-enriched peptide table

manual_impute(): Imputation by random draws from a manually defined distribution

meanSdPlot(): Plot row standard deviations versus row means

normalize_pe(): Normalize a QFeatures object

normalize_vsn(): Normalization using vsn

ntf_deg(): Assign normalized assay for DEGdata object

pe2se(): Extract the proteins SummarizedExperiment object from a QFeatures container

plot_Tsne(): Plot t-Sne

plot_cond(): Plot frequency of significant conditions per protein and the overlap in proteins between conditions

plot_cond_freq(): Plot frequency of significant conditions per protein

plot_cond_overlap(): Plot conditions overlap

plot_cor(): Plot correlation matrix

plot_coverage(): Plot protein coverage

plot_cvs(): Plot sample coefficient of variation whitin group

plot_detect(): Visualize intensities of proteins with missing values

plot_diff_hist(): Fit a Gaussian distribution for L2FC of each contrast

plot_dist(): Plot Gower's distance matrix

plot_frequency(): Plot protein overlap between samples

plot_heatmap(<SummarizedExperiment>) plot_heatmap(<DEGdata>): Plot a heatmap

plot_imputation(): Visualize imputation

plot_ma_RNA(): MA-plot of RNA expression data

plot_ma_pro(): MA-plot of quantity data

plot_missval(): Plot a heatmap of proteins with missing values

plot_multi_heatmap(): Plot heatmap of specified genes/proteins across multiple omics results

plot_multi_venn(): Plot venn plot of specified genes/proteins across multiple omics results

plot_norm_distribution(): Plot the fit normal for log2 fold change

plot_normalization(): Visualize normalization

plot_numbers(): Plot protein numbers

plot_pca(): Plot PCA

plot_single(): Plot values for a protein/gene of interest

plot_statistics(): Plot the distribution of statistic valuse. develop from statistics_plot

plot_umap(): Plot Tsne

plot_volcano(): Volcano plot

reshape_long2wide(): Reshape a long table to wide

rlg_deg(): Assign a rlog transformed assay for DEGdata object

run_app(): Run shiny application in DEP2

test_GSEA(): GSEA data

test_ORA(): ORA for differenatial test result

test_PPI(): Protein-protein interaction analysis

test_diff(): Differential enrichment/expression test

test_diff_deg(): Differential expression test on a DESeqDataSet

theme_DEP1(): DEP ggplot theme 1

theme_DEP2(): DEP ggplot theme 2