uSORT_sorting_wrapper: wrapper of all avaliable sorting methods in uSORT
In uSORT: uSORT: A self-refining ordering pipeline for gene selection

Description Usage Arguments Value Examples

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 `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.

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')