Package index • jamses

All functions

SEDesign(): SEDesign: experiment design and contrasts object (S7 class)
SEStats(): SEStats S7 Object
check_sedesign(): Check SEDesign object
choose_annotation_colnames(): Choose interesting annotation colnames from a data.frame
combine_sestats(): Combine SEStats objects by contrast,signal
contrast2comp() comp2contrast() names_contrast2comp() names_comp2contrast(): Convert contrast to short-form comp, convert comp to contrast
contrast2comp_dev(): Convert contrast to short-form comp, convert comp to contrast (DEV)
contrast_colors_by_group(): Define contrast colors by group colors
contrast_names(): Get contrast names from SEStats
contrast_names_to_sedesign(): Convert contrast names to sedesign object
contrastnames() `contrastnames<-`() contrast_names() `contrast_names<-`(): Contrast names for SEDesign objects
`contrasts<-`(): Contrast matrix setter for SEDesign objects
contrasts(): Contrast matrix accessor for SEDesign objects
contrasts_to_factors(): Convert contrasts to data.frame of design factors
contrasts_to_venn_setlists(): Convert contrast names to Venn setlists for visual comparison
design(<SEDesign>) `design<-`(<SEDesign>,<matrix>): Design matrix accessor for SEDesign objects
detect_heatmap_components(): Detect ComplexHeatmap Heatmap grid layout components
dim(): Get dimensions for SEDesign
dimnames(): Get dimnames from SEDesign
dimnames(): Get dimnames from SEStats
draw_oneway_contrast(): Draw one-way contrast using block arrows
draw_twoway_contrast(): Draw two one-way contrasts using block arrows, showing a two-way connector
ebayes2dfs(): Convert limma eBayes fit to data.frame with annotated hits
factors(): Get factor names from SEStats
factors() `factors<-`(): Experimental factor labels for SEDesign objects
filter_contrast_names(): Filter contrast names
fold_to_log2fold(): Convert normal signed fold change to log2 fold change
format_hits(): Format list of hit vectors into summary counts
geomx_to_se(): Convert NanoStringGeoMxSet to SummarizedExperiment
groups(): Get groups from SEStats
groups() `groups<-`(): Design group names for SEDesign objects
groups_to_sedesign(): Create SEDesign from experimental groups
handle_na_values(): Handle NA values in a numeric matrix
heatmap_column_group_labels(): Add Heatmap column group labels
heatmap_profile_plot(): Profile Line Plot for Heatmap of SummarizedExperiment data
heatmap_se(): Heatmap for SummarizedExperiment data
hit_array_to_list(): Quick conversion of hit_array to hit_list
intercalate(): Intercalate two or more vectors
list2im_opt(): Convert list to incidence matrix
list2im_value_internal(): List to value incidence matrix
list_to_sestats(): Prepare SEStats from a list of stat data.frame
log2fold_to_fold(): Convert log2 fold change to signed fold change
make_block_arrow_polygon(): Make block arrow polygon coordinates for line segments
make_se_test(): Make SummarizedExperiment test data
mark_stat_hits(): Mark statistical hits by threshold cutoffs
matrix_normalize(): Normalize a numeric data matrix
merge_statdf_all_test(): Merge stats data.frame from two sestats results
plot(<SEDesign>): Plot method for SEDesign objects
plot_sedesign(): Plot sedesign object contrasts
point_handedness(): Determine which side one point is to another, given a slope or angle
point_slope_intercept(): convert point-slope to axis intercept
print(): Print / show method for SEDesign objects
print(): Print SEStats Object
process_sestats_to_hitim(): Process sestats input into a hit incidence matrix
run_limma_replicate(): Run limma contrasts with optional probe replicates
samples(): Get samples from SEStats
samples() `samples<-`(): Sample identifiers for SEDesign objects
save_sestats(): Save SE contrast stats output
se_collapse_by_column(): Collapse SummarizedExperiment data by column
se_collapse_by_row(): Collapse SummarizedExperiment data by row
se_contrast_stats(): Compute contrast statistics on SummarizedExperiment data
se_detected_rows(): SummarizedExperiment heuristics to define detected rows
se_normalize(): Normalize SummarizedExperiment data
se_rbind(): Combine SummarizedExperiment objects by row
se_to_assay_data(): Get SE assay data
se_to_assay_names(): Get SE assay names
se_to_rowcoldata(): Get SE colData and rowData
sedesign_to_factors(): Convert SEDesign to data.frame of design factors
sestats_to_df(): Convert sestats to table summary
shortest_unique_abbreviation(): Find the shortest abbrevation to retain unique values
shrinkDataFrame(): Shrink data.frame by row groups
shrink_df(): Shrink data.frame by row groups
shrink_matrix(): Shrink a numeric matrix by groups of rows
simulate_se_test(): Simulate SummarizedExperiment tests
sort_contrasts(): Sort contrasts by factor and level
sort_samples(): Sort biological sample labels for experimental design
stack_contrasts(): Stack a vector of contrasts into a full string
strsplitOrdered(): Split the elements of an ordered factor vector
`[`: Subset a SEDesign object by samples and/or design groups
sub_split_vector(): Sub-split a split vector (Internal)
update_function_params(): Update function default parameters
update_list_elements(): Update a subset of list elements
validate_sedesign(): Validate SEDesign object contents
voom_jam(): Limma-voom customized for Jam