uSORT {uSORT} | R Documentation |
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.
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)
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 |
refine_sorting_method |
Method name for refined sorting, including |
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 |
pre_SPIN_option |
SPIN contains two options including |
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 |
ref_SPIN_option |
SPIN contains two options including |
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. |
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
.
results object (a list)
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)