Package index

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

annotateSegments()

Annotate consensus segments across cluster with CNA states

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)