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 testing whether the single cells from different data types 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.

This function is used for testing whether the single cells from different data types 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.

Usage

neighbor_test(input_data, ref_data, dist_scale = 10,
  print_message = TRUE)

neighbor_test(input_data, ref_data, 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).
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).
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

input_count	The number of cells in the input data for each test.
ref_count	The number of cells in the reference data for each test.
pval	P-values from fisher's extract tests.
input_count	The number of cells in the input data for each test.
ref_count	The number of cells in the reference data for each test.
pval	P-values from fisher's extract tests.

Examples

## Not run: 
neighbor_test_p <- neighbor_test(input_data,ref_data,dist_scale=10)$pval

## End(Not run)
## Not run: 
neighbor_test_p <- neighbor_test(input_data,ref_data,dist_scale=10)$pval

## End(Not run)

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