Package index • muscadet

Object creation and manipulation

Objects, classes and methods

Classes and functions to create muscomic/muscadet objects and data access

CreateMuscomicObject(): Create a muscomic object

muscomic-class muscomic: The muscomic class

CreateMuscadetObject(): Create a muscadet object

muscadet-class muscadet: The muscadet class

coordFeatures() matCounts() matLogRatio() Cells(<muscomic>) Cells(<muscadet>) Features(<muscomic>) Features(<muscadet>): Methods for muscomic and muscadet objects

`[`(<muscadet>) `[`(<muscomic>) `$`(<muscadet>) `$`(<muscomic>) `[<-`(<muscadet>) `[<-`(<muscomic>) `$<-`(<muscadet>) `$<-`(<muscomic>): Access and assignment methods for muscadet objects

.DollarNames(<muscadet>) .DollarNames(<muscomic>): Autocompletion for $ access on muscadet or muscomic objects

Object incremental additions

Functions for incremental additions to muscadet objects during analysis

addAlleleCounts(): Add allele counts to a muscadet object

assignClusters(): Assign a cluster assignment to a muscadet object

Log-ratio computation

Functions to compute log R ratios from the count matrices (coverage information)

computeLogRatio(): Compute log R ratios

computeLogRatioATAC(): Compute log R ratios for scATAC-seq data

computeLogRatioRNA(): Compute log R ratios for scRNA-seq data

getLogRatioBulk(): Retrieve log R ratio from Bulk data on single-cell features (internal)

Integration and clustering

Functions to integrate log-ratios of omics and cluster cells

clusterMuscadet(): Multi Omics Integration and Clustering on a muscadet Object

cluster_seurat(): Multi Omics Clustering using Seurat Multi Modal Graph-based Clustering

cluster_hclust(): Multi Omics Clustering with SNF integration and Hierarchical Clustering

weightedSNF(): Weighted Similarity Network Fusion

imputeClusters(): Impute cluster assignments for missing cells by similarity

Visualization - log-ratios and clusters

Functions to visualize log-ratios data on chromosomes, clusters of cells, and usefull for clustering validation

heatmapStep(): Create heatmap and distribution plots of the different steps of computing log R ratios

heatmapMuscadet(): Heatmap plot for muscadet object

plotSil(): Silhouette plot for muscadet object

plotIndexes(): Plot clustering validation indexes for a muscadet object

plotUMAP(): Plot UMAP Coordinates from a muscadet Object

add_labels(): Add Labels to a ggplot Object

Calling of Copy Number Alterations

Functions to identify Copy Number Alterations

mergeCounts(): Merge counts for muscadet objects

cnaCalling(): Copy Number Alteration (CNA) Calling from muscadet object

preProcSample2(): Process read count matrix and segmentation

getSegConsensus(): Get consensus segments across clusters

Visualization - Copy Number Alterations profiles

Functions to visualize Copy Number Alterations profiles at clone-level and sample-level

plotProfile(): Plot CNA profiles from muscadet object

plotCNA(): Plot CNA segments across clusters from a muscadet object

Data preparation

Functions facilitating allelic data preparation

process_allele(): Process allele counts results from SCReadCounts format

save_as_vcf(): Save a data frame as a VCF File

Example data

Example data used for examples and practicing functions

muscadet_obj muscadet_obj_ref: Example data: muscadet objects

mat_counts_atac_tumor mat_counts_atac_ref mat_counts_rna_tumor mat_counts_rna_ref: Example data: Matrices of raw counts

allele_counts_atac_tumor allele_counts_atac_ref allele_counts_rna_tumor allele_counts_rna_ref: Example data: Allele counts at variation positions

genes peaks: Example data: Feature coordinates

bulk_lrr: Example data: Log R ratio from bulk sequencing data

Misc

genome_chrom hg38_chrom hg19_chrom mm10_chrom: Genome chromosome sizes (internal data)