cellMap: cellMap

In zhupinglab/Aodav: Advanced omics data analysis and visualization

Description

Map single cells to each cell clusters. This functions embeds 'scmap' tool and improves to enable multiple rounds of projection to increase the mapping accuracy of cells with similar experssion patterns.

Usage

cellMap(ref, data, map = NULL, pvalue = NULL, adjP = 0.05,
  fc = 0.25, threshold = 0.7, method = "pwDEG")

Arguments

ref	Seurat object with defined clusters stored in ref@ident as a reference.
data	Seurat object with cells to be mapped to the reference.
map	list of clusters to map accordingly. Defualt is NULL to use all clusters in ref@ident.
pvalue	p value to filter genes used for index construction.
adjP	adjusted p value to filter genes used for index construction only if pvalue is NULL.
fc	fold change of expression to filter genes used for index construction.
threshold	similarity threshould for mapping cells to clusters.
method	strategy for gene selection. Default is "pwDEG". In case few genes were selected, the "selectFeatures" function in scmap is also implemented to select 200 genes.

Examples

## Not run: 
round1 <- c("CD4-C1-CCR7", "CD4-C2-SELL", "CD4-C3-CD82", "CD4-C4-GZMH")
round2 <- c("CD4-C1-CCR7", "CD4-C2-SELL")
projection <- cellMap(ctrl.cd4T.obj, ctrl.cd4T.obj, map=list(round1, round2), threshold=0.3)
table(ctrl.cd4T.obj@ident)
table(projection$round1$scmap_cluster_labs)
table(projection$round2$scmap_cluster_labs)

## End(Not run)

zhupinglab/Aodav documentation built on June 10, 2019, 2:31 a.m.