uSORT_sorting_wrapper: wrapper of all avaliable sorting methods in uSORT

Description Usage Arguments Value Examples

View source: R/uSort_sorting_wrapper.R

Description

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

Usage

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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

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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')

uSORT documentation built on May 31, 2017, 11:39 a.m.