Instructions.md

In TrakhtenbergLab/CellTools: CellTools

Instruction

Read reference and query seurat object files into the R

reference <- readRDS(“/path-to-referencedata”) 
query <- readRDS(“/path-to-querydata”) 

The reference and query seurat objects need to be pre-processed with standard pre-processing workflow for scRNA-seq data in Seurat.

Find the optimal k-weight parameter for KNN

This function iterates through a select range of k-weight parameters and stores the optimal parameter in the Seurat object

reference <- OptiK(reference, lab = "type", range = c(5,50), dims = 50, perc = 0.2)

• @param data Reference Seurat object
• @param lab The reference label to treat as clusters. Default is "seurat_clusters"
• @param range The range of k-weight values to loop through. Default is 10-100.
• @param dims The number of PCs to consider when discovering anchors
• @param perc The percent of cells to subsample from the refeerence for the test query. Default is 20%.
• @param num If perc = F, OptiK will look for a specific number of cells specified here.
• @param seed Set the seed for reproducible results. Default = 1984.
• @return Returns a Seurat object with a new slot where the k-weight is stored: misc$CellTools$opti_k

Denoise a reference Seurat Object

reference<- DeNoise(ref, lab = "type", coef = 1.5)

• @param ref: Reference Seurat object with pre-calculated UMAP
• @param lab: The reference label to treat as clusters. Default is "seurat_clusters"
• @param coef: The coefficient to multiply by the IQR. Default is 1.5
• @return: Returns a Seurat object with a new slot called "denoise"

Map query Seurat object to reference Seurat object

This function is a wrapper for Seurat's TransferData, IntegrateEmbeddings, and ProjectUMAP functions, meant to be run after

Result<- MapTo(ref, query, lab = "type", dims = 50)

• @param ref Reference Seurat object
• @param query Wuery Seurat object
• @param lab The reference label to treat as clusters. Default is "seurat_clusters"
• @param k The k-weight to use when weighting anchors. Default is opti
• @param get.anchors A logical that when true will first run Seurat's FindTransferAnchors. Default is TRUE.
• @param dims Number of PCs to use when get.anchors = T. Default is 30
• @return Returns a Seurat object with a new slot where the k-weight is stored: misc$CellTools$opti_k

Optimized Tracing of Query to Reference Data

This function examines the global transcriptomic properties of single cell data.

correlation<-GlobalProbe(dat,lab="type")

• @param dat A Seurat object
• @param lab The reference @meta.data slot on which to compare global parameters
• @return Global correlation analyses of the clusters provided in lab parameter

TrakhtenbergLab/CellTools documentation built on Aug. 21, 2023, 2:39 p.m.