uSort: uSORT: A self-refining ordering pipeline for gene selection

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

Description

This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data.

The main function of uSORT-pacakge which provides a workflow of sorting scRNA-seq data.

Usage

uSORT(exprs_file, log_transform = TRUE, remove_outliers = TRUE,
  preliminary_sorting_method = c("autoSPIN", "sWanderlust", "monocle",
  "Wanderlust", "SPIN", "none"), refine_sorting_method = c("autoSPIN",
  "sWanderlust", "monocle", "Wanderlust", "SPIN", "none"),
  project_name = "uSORT", result_directory = getwd(), nCores = 1,
  save_results = TRUE, reproduce_seed = 1234,
  scattering_cutoff_prob = 0.75, driving_force_cutoff = NULL,
  qval_cutoff_featureSelection = 0.05, pre_data_type = c("linear",
  "cyclical"), pre_SPIN_option = c("STS", "neighborhood"),
  pre_SPIN_sigma_width = 1, pre_autoSPIN_alpha = 0.2,
  pre_autoSPIN_randomization = 20, pre_wanderlust_start_cell = NULL,
  pre_wanderlust_dfmap_components = 4, pre_wanderlust_l = 15,
  pre_wanderlust_num_waypoints = 150, pre_wanderlust_waypoints_seed = 2711,
  pre_wanderlust_flock_waypoints = 2, ref_data_type = c("linear",
  "cyclical"), ref_SPIN_option = c("STS", "neighborhood"),
  ref_SPIN_sigma_width = 1, ref_autoSPIN_alpha = 0.2,
  ref_autoSPIN_randomization = 20, ref_wanderlust_start_cell = NULL,
  ref_wanderlust_dfmap_components = 4, ref_wanderlust_l = 15,
  ref_wanderlust_num_waypoints = 150, ref_wanderlust_flock_waypoints = 2,
  ref_wanderlust_waypoints_seed = 2711)

Arguments

exprs_file	Input file name in txt format, with rownames of cells and colnames of genes.
log_transform	Boolean, if log transform the data.
remove_outliers	Boolean, if remove the outliers.
preliminary_sorting_method	Method name for preliminary sorting, including autoSPIN, sWanderlust, monocle, Wanderlust, SPIN, or none.
refine_sorting_method	Method name for refined sorting, including autoSPIN, sWanderlust, monocle, Wanderlust, SPIN, or none.
project_name	A character name as the prefix of the saved result file.
result_directory	The directory indicating where to save the results.
nCores	Number of cores that will be employed for drive gene selection (parallel computing), default is 1.
save_results	Boolean determining if save the results.
reproduce_seed	A seed used for reproducing the result.
scattering_cutoff_prob	Scattering cutoff value probability for gene selection, default 0.75.
driving_force_cutoff	Driving force cutoff value for gene selection, default NULL(automatically).
qval_cutoff_featureSelection	Q value cutoff for gene selection, default 0.05.
pre_data_type	The data type which guides the autoSPIN sorting, including linear, cyclical.
pre_SPIN_option	SPIN contains two options including STS(default), neighborhood.
pre_SPIN_sigma_width	Sigma width parameter for SPIN, default is 1.
pre_autoSPIN_alpha	alpha parameter for autoSPIN, default is 0.2.
pre_autoSPIN_randomization	Number of randomizations for autoSPIN, default is 20.
pre_wanderlust_start_cell	The name of starting cell for wanderlust, default is the first cell from the data.
pre_wanderlust_dfmap_components	Number of components from diffusion map used for wanderlust analysis, default is 4.
pre_wanderlust_l	Number of nearest neighbors used for wanderlust, default is 15.
pre_wanderlust_num_waypoints	Number of waypoint used for wanderlust, default is 150.
pre_wanderlust_waypoints_seed	The seed for reproducing the wanderlust results.
pre_wanderlust_flock_waypoints	The number of times for flocking the waypoints, default is 2.
ref_data_type	The data type which guides the autoSPIN sorting, including linear, cyclical.
ref_SPIN_option	SPIN contains two options including STS(default), neighborhood.
ref_SPIN_sigma_width	Sigma width parameter for SPIN, default is 1.
ref_autoSPIN_alpha	alpha parameter for autoSPIN, default is 0.2.
ref_autoSPIN_randomization	Number of randomizations for autoSPIN, default is 20.
ref_wanderlust_start_cell	The name of starting cell for wanderlust, default is the first cell from the data.
ref_wanderlust_dfmap_components	Number of components from diffusion map used for wanderlust analysis, default is 4.
ref_wanderlust_l	Number of nearest neighbors used for wanderlust, default is 15.
ref_wanderlust_num_waypoints	Number of waypoint used for wanderlust, default is 150
ref_wanderlust_flock_waypoints	The number of times for flocking the waypoints, default is 2.
ref_wanderlust_waypoints_seed	The seed for reproducing the wanderlust results.

Details

This package incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization. The uSORT workflow can be implemented through calling the main function or the GUI. uSORT.

Value

results object (a list)

See Also

uSORT-package, uSORT_GUI

Examples

dir <- system.file('extdata', package='uSORT')
file <- list.files(dir, pattern='.txt$', full=TRUE)
#remove the # symbol of the following codes to test
#uSORT_results <- uSORT(exprs_file = file, project_name = "test",
# preliminary_sorting_method = "autoSPIN",
# refine_sorting_method = "sWanderlust",
# save_results = FALSE)

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