uSORT_sorting_wrapper {uSORT} | R Documentation |
Sorting methods include autoSPIN
, sWanderlust
, monocle
,
Wanderlust
, SPIN
. Any of the sorting method can be called directly
using this funciton.
uSORT_sorting_wrapper(data, data_raw, method = c("autoSPIN", "sWanderlust", "monocle", "Wanderlust", "SPIN", "none"), data_type = c("linear", "cyclical"), SPIN_option = c("STS", "neighborhood"), SPIN_sigma_width = 1, autoSPIN_alpha = 0.2, autoSPIN_randomization = 20, wanderlust_start_cell = NULL, wanderlust_dfmap_components = 4, wanderlust_l = 15, wanderlust_num_waypoints = 150, wanderlust_waypoints_seed = 2711, wanderlust_flock_waypoints = 2)
data |
Input preprocessed data matrix with row.name of cells and col.name of genes. |
data_raw |
Input raw data matrix with row.name of cells and col.name of genes, for monocle method. |
method |
The name of the sorting method to use, including |
data_type |
The type of the data, either |
SPIN_option |
The runing option of SPIN, |
SPIN_sigma_width |
Sigma width for SPIN. |
autoSPIN_alpha |
alpha for autoSPIN. |
autoSPIN_randomization |
Number of randomization for autoSPIN. |
wanderlust_start_cell |
The id of the starting cell for wanderlust. |
wanderlust_dfmap_components |
The number of components from diffusionmap for wanderlust. |
wanderlust_l |
The number of nearest neighbors used for wanderlust. |
wanderlust_num_waypoints |
The number of waypoints for wanderlust. |
wanderlust_waypoints_seed |
The seed for reproducible analysis. |
wanderlust_flock_waypoints |
The bumber of flock times for wanderlust. |
return the order of sorting results.
dir <- system.file('extdata', package='uSORT') file <- list.files(dir, pattern='.txt$', full=TRUE) exprs <- uSORT_preProcess(exprs_file = file) exp_trimmed <- t(exprs$exprs_log_trimed) PCA_selected_genes <- pca_gene_selection(exp_trimmed) exp_PCA_genes <- exp_trimmed[, PCA_selected_genes] #order <- uSORT_sorting_wrapper(data = exp_PCA_genes, method = 'autoSPIN')