eval_neighbor_test: Evaluate the spacial discribution of the mixed single cells...

In WeiqiangZhou/SINTER: Single-cell genomic data integration

Description

This function is used for evaluating whether single cells from the same cell type are mixed well. For each cell in the input data, a fisher's extract test will be performed to test whether the ratio of input cells to reference cells in the given region is the same as the ratio of the total number of input cells to the total number of reference cells while only single cells from the same cell type are considered.

This function is used for evaluating whether single cells from the same cell type are mixed well. For each cell in the input data, a fisher's extract test will be performed to test whether the ratio of input cells to reference cells in the given region is the same as the ratio of the total number of input cells to the total number of reference cells while only single cells from the same cell type are considered.

Usage

eval_neighbor_test(input_data, ref_data, input_mem, ref_mem,
  dist_scale = 10, print_message = TRUE)

eval_neighbor_test(input_data, ref_data, input_mem, ref_mem,
  dist_scale = 10, print_message = TRUE)

Arguments

input_data	Low dimensional representation of single cell from one data type as the input for matching (e.g., PCs from scRNA-seq data).
ref_data	Low dimensional representation of single cell from another data type as the reference for matching (e.g., PCs from scATAC-seq data).
input_mem	Cell type label for the input_data.
ref_mem	Cell type label for the ref_data.
dist_scale	Scale used to define the radius of the region for testing.
print_message	Flag to print the radius used for the testing.
input_data	Low dimensional representation of single cell from one data type as the input for matching (e.g., PCs from scRNA-seq data).
ref_data	Low dimensional representation of single cell from another data type as the reference for matching (e.g., PCs from scATAC-seq data).
input_mem	Cell type label for the input_data.
ref_mem	Cell type label for the ref_data.
dist_scale	Scale used to define the radius of the region for testing.
print_message	Flag to print the radius used for the testing.

Value

test_stat	P-values from fisher's extract tests.
test_stat	P-values from fisher's extract tests.

Examples

## Not run: 
test_stat <- eval_neighbor_test(input_data,ref_data,input_mem,ref_mem,dist_scale=10,print_message=TRUE)

## End(Not run)
## Not run: 
test_stat <- eval_neighbor_test(input_data,ref_data,input_mem,ref_mem,dist_scale=10,print_message=TRUE)

## End(Not run)

WeiqiangZhou/SINTER documentation built on Sept. 11, 2019, 8:03 a.m.