Man pages for xzhoulab/SPARK
Spatial Pattern Recognition via Kernels
| ACAT | Combining P values for all kernels (Vector-Based) |
| CombinePValues | Summarized the multiple p-values via Cauchy combination rule |
| ComputeGaussianL | Compute Gaussian kernel matrix |
| ComputeGaussianPL | Calculate Gaussian Parameter L based on Eculidean Distance |
| ComputeTestQuantRcpp_cov | Compute the testing quantities with covariates, float format |
| ComputeTestQuantRcpp_Gaussian | Compute the testing quantities for linear mixed model, float... |
| ComputeTestQuantRcpp_nocov | Compute the testing quantities without covariates, float... |
| ComputeWeightsRcpp | Compute the kernel weights using psedu-counts |
| CovariatesAI | Variance component estimation with covariates using Average... |
| CreateSPARKObject | Create the SPARK object with filtering step |
| ED_cpp | Compute Euclidean distance matrix by rows |
| FilteringGenesCells | Filtering out the genes that are lowly expressed acorss cells... |
| noCovariatesAI | Variance component estimation without covariates using... |
| NormalizeVST | Anscombe variance stabilizing transformation: NB |
| NormalizeVSTfast | Anscombe variance stabilizing transformation (Time Efficient) |
| rcpp_hello_world | Simple function using Rcpp |
| spark.ai | Fitting the count-based spatial model using average... |
| SPARK-class | Each SPARK object has a number of slots which store... |
| spark.fit | Fitting the count-based spatial model to estimate the... |
| sparkg_sw | Fast Test for the Gaussian version of SPARK through... |
| sparkg_sw_sk | Test for single kernel in the fast version of SPARK-G |
| SPARK-package | Spatial Pattern Recognition via Kernels |
| spark.test | Testing multiple kernel matrices |
| spark.test_each | Testing one kernel matrix to identify spatial pattern |
| spark.vc | Fitting the count-based spatial model to estimate the... |
| spark.weights | Computing gene specific weights for combining multiple... |
| sparkx | The main function that testing multiple kernels with... |
| sparkx_pval | Calculate SPARK-X P-values |
| sparkx.sk | Testing for single kernel with non-parametric framework |
| sparkx.sksg | Testing for single gene with each kernel with non-parametric... |
| SparseSysMatEigen | Do inverse of sparse sysmetric matrix |
| sp_means_Rcpp | Calculate column-wise or row-wise mean |
| sp_nz_count_Rcpp | Count column-wise or row-wise non-zero elements of sparse... |
| sp_sums_Rcpp | Calculate column-wise or row-wise sum |
| sp_vars_Rcpp | Calculate column-wise or row-wise variance |
| SysMatEigen | Do inverse of sysmetric matrix |
| transloc_func | Transforming the coordinate |
