Evolutionary Transcriptomics

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Documentation for package ‘myTAI’ version 2.3.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

age.apply	Age Category Specific apply Function
as_BulkPhyloExpressionSet	as_BulkPhyloExpressionSet
as_data_frame	Convert BulkPhyloExpressionSet to Data Frame
BulkPhyloExpressionSet	Bulk PhyloExpressionSet Class
BulkPhyloExpressionSet_from_df	Convert Data to BulkPhyloExpressionSet
check_BulkPhyloExpressionSet	Check if object is a BulkPhyloExpressionSet
check_PhyloExpressionSet	Check if object is a PhyloExpressionSet
check_ScPhyloExpressionSet	Check if object is a ScPhyloExpressionSet
collapse	Collapse PhyloExpressionSet Replicates
ConservationTestResult	Conservation Test Result S7 Class
COUNT_TRANSFORMS	Count Transformation Functions
destroy_pattern	Destroy Phylotranscriptomic Pattern Using GATAI
diagnose_test_robustness	Diagnose Test Robustness
Distribution	Distribution S7 Class
distributions	Predefined Distribution Objects
downsample	Downsample ScPhyloExpressionSet
downsample_expression	Downsample Expression Matrix by Groups
example_phyex_set	Example phyex set
example_phyex_set_old	Example phyex set old
example_phyex_set_sc	Load Example Single-Cell PhyloExpressionSet
exp_p	Format P-Value for Scientific Notation
gatai_animate_destruction	Animate GATAI Destruction Process
genes_lowly_expressed	Select Lowly Expressed Genes
genes_top_expr	Gene Expression Filtering Functions
genes_top_mean	Select Top Mean Expressed Genes
genes_top_variance	Select Top Variable Genes
match_map	Match Gene Expression Data with Phylostratum Map
match_map_sc_matrix	Match Expression Matrix with Phylostratum Map
match_map_sc_seurat	Match Single-Cell Expression Data with Phylostratum Map (Seurat)
normalise_stage_expression	Normalise Stage Expression Data
omit_matrix	Compute TXI Profiles Omitting Each Gene
permute_PS	Permute Strata in PhyloExpressionSet
PhyloExpressionSetBase	PhyloExpressionSet Base Class
plot_contribution	Plot Phylostratum Contribution to Transcriptomic Index
plot_cullen_frey	Plot Cullen-Frey Diagram for Distribution Assessment
plot_distribution_expression	Comparing expression levels distributions across developmental stages
plot_distribution_pTAI	Partial TAI Distribution Plotting Functions
plot_distribution_pTAI_qqplot	QQ plot comparing partial TAI distributions across developmental stages against a reference stage
plot_distribution_strata	Plot Distribution of Genes Across Phylostrata
plot_gatai_results	Plot Comprehensive GATAI Results
plot_gene_heatmap	Plot Gene Expression Heatmap
plot_gene_profiles	Plot Individual Gene Expression Profiles
plot_gene_space	Plot Gene Space Using PCA
plot_mean_var	Plot Mean-Variance Relationship
plot_null_txi_sample	Plot Null TXI Sample Distribution
plot_relative_expression_bar	Plot Mean Relative Expression Levels as Barplot
plot_relative_expression_line	Plot Relative Expression Profiles (Line Plot)
plot_sample_space	Plot Sample Space Visualization
plot_signature	Plot Transcriptomic Signature
plot_signature_gene_quantiles	Plot Signature Across Gene Expression Quantiles
plot_signature_multiple	Plot Multiple Transcriptomic Signatures
plot_signature_transformed	Plot Signature Under Different Transformations
plot_strata_expression	Plot Expression Levels by Phylostratum
PS_colours	Generate Phylostratum Colors
pTXI	Calculate Phylostratum-Specific Transcriptomic Index
quantile_rank	Calculate Quantile Ranks
relative_expression	Relative Expression Functions
rel_exp_matrix	Compute Relative Expression Matrix for PhyloExpressionSet
remove_genes	Remove Genes from PhyloExpressionSet
rename_phyex_set	Rename a PhyloExpressionSet
save_gatai_results_pdf	Save GATAI Analysis Results to PDF
ScPhyloExpressionSet	Single-Cell PhyloExpressionSet Class
ScPhyloExpressionSet_from_matrix	Create Single-Cell PhyloExpressionSet from Expression Matrix
ScPhyloExpressionSet_from_seurat	Convert Seurat Object to Single-Cell PhyloExpressionSet
select_genes	Select Genes from PhyloExpressionSet
set_expression	Gene Expression Transformation Functions
stat_early_conservation_test	Early Conservation Test
stat_flatline_test	Flat Line Test for Conservation Pattern
stat_generic_conservation_test	Generic Conservation Test Framework
stat_late_conservation_test	Late Conservation Test
stat_pairwise_test	Pairwise Conservation Test
stat_reductive_hourglass_test	Reductive Hourglass Test
stat_reverse_hourglass_test	Reverse Hourglass Test
strata_enrichment	Calculate Phylostratum Enrichment
sTXI	Calculate Stratum-Specific Transcriptomic Index
TAI	Calculate Transcriptomic Age Index (TAI)
taxid	Retrieve taxonomy categories from NCBI Taxonomy
TDI	Calculate Transcriptomic Divergence Index (TDI)
TEI	Calculate Transcriptomic Evolutionary Index (TEI)
TestResult	Test Result S7 Class
tf	Short Alias for Transform Counts
tf_PS	Transform Phylostratum Values
tf_stability	Perform Permutation Tests Under Different Transformations
TI_map	Transcriptomic Index Name Mapping
TPI	Calculate Transcriptomic Polymorphism Index (TPI)
transform_counts	Transform Expression Counts in PhyloExpressionSet
TXI	Calculate Transcriptomic Index (TXI)
TXI_conf_int	Confidence Intervals for Transcriptomic Index (TXI)
TXI_std_dev	Standard Deviation for TXI