uSORT_sorting_wrapper: wrapper of all avaliable sorting methods in uSORT

In JinmiaoChenLab/uSORT: uSORT: A self-refining ordering pipeline for gene selection

Description

Sorting methods include autoSPIN, sWanderlust, monocle, Wanderlust, SPIN. Any of the sorting method can be called directly using this funciton.

Usage

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)

Arguments

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 autoSPIN, sWanderlust, monocle, Wanderlust, SPIN and none.
data_type	The type of the data, either linear or cyclical.
SPIN_option	The runing option of SPIN, STS or neighborhood.
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.

Value

return the order of sorting results.

Examples

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')

JinmiaoChenLab/uSORT documentation built on May 7, 2019, 10:53 a.m.