scHiC_assess: This function analyzes both simulated and real datasets,...

In Queen0044/HiCImpute: HiCImpute: An R Package Implementing "Bayesian Hierarchical Model for Identifying Structural Zeros and Enhancing Single-cell Hi-C Data"

This function analyzes both simulated and real datasets, depending on the inputs of the functions.

Description

This function analyzes both simulated and real datasets, depending on the inputs of the functions.

Usage

scHiC_assess(
  scHiC,
  expected = NULL,
  result = NULL,
  imputed = NULL,
  cell_index = 1,
  n,
  cell_type,
  dims = 2,
  perplexity = 10,
  seed = 1000,
  kmeans = TRUE,
  ncenters = 2
)

Arguments

scHiC	The observed data. It can take three types of formats. The preferred format is a single-cell matrix with each column being a vector of the upper triangular matrix without including the diagonal entries of the 2D matrix of a single-cell. Another types of formats are a list with each element being a 2D s ingle-cell contact matrix, or a 3D (n\times n\times k) array that has k matrices of dimension n\times n. HiCImpute automatically transforms these two types of input into a matrix with each column being the vector of upper triangular matrix of a single-cell.
expected	Underline true counts of the simulated data. For real data analysis, just set it as NULL.
result	Output of MCMCImpute.
imputed	The imputed data that has the same dimension as the observed data. This is needed for real data analysis. For simulated data, set it as NULL.
cell_index	Indicates which cell is used to draw heatmaps and scatterplot.
n	Dimension of 2D contact matrix.
cell_type	A vector of underlying true cluster.
dims	The dimension of 2D matrix.
perplexity	numeric; Perplexity parameter (should not be bigger than 3\times perplexity<nrow(X)-1).
seed	Random seed for generating t-SNE data.
kmeans	Logical, whether apply K-means clustering on the t-SNE data.
ncenters	Number of centers in K-means clustering analysis.

Value

A list of accuracy measurements and plots.

Examples

data("K562_1_true")
options(digits = 2)
scHiC_assess(scHiC=K562_T1_7k, expected=K562_1_true, imputed=result$Impute_SZ=T1_7k_imp)

Queen0044/HiCImpute documentation built on Oct. 9, 2022, 9:30 a.m.