do_salsa_steps: Perform SALSA steps for threshold detection
In jmw86069/salsa: Single-cell Amalgamation by Latent Semantic Analysis (SALSA)

Description Usage Arguments Details Value See Also Examples

Perform SALSA steps for threshold detection

do_salsa_steps(x, n_vector = NULL, n_start = NULL, max_step = NULL,
  step_size = NULL, count_vector = NULL, dists = c("frechet",
  "frechet-weibull"), cache_fr = cache_filesystem("./cache_fr"),
  cache_fr_wei = cache_filesystem("./cache_fr_wei"),
  param_fr_wei = NULL, fr_method = "mme", fr_wei_method = c("mle",
  "mge"), do_shiny_progress = FALSE, verbose = FALSE, ...)

`x`	numeric vector of counts, either the number of UMI per cell, or the number of UMI per gene.
`n_vector, n_start, max_step, step_size, count_vector`	arguments passed to `get_salsa_steps()` which returns `count_vector`. If `count_vector` is supplied, it is used without modification.
`dists`	character vector determining which distribution fit functions to calculate, `"frechet"` fits the Frechet distribution, `"frechet-weibull"` fits the five-parameter combined Frechet and Weibull distributions. Typically the Frechet parameters are used to define the upper bound, and the Frechet-Weibull parameters are used to define the lower bound.
`cache_fr, cache_fr_wei`	list objects output from `memoise::cache_filesystem()` used to store cached distribution fit results. When either are NULL, the memoise cache steps are disabled, and the functions are called directly.
`param_fr_wei`	`data.frame` output from `params_fr_wei()` which defines the parameter upper and lower limits, and start values for each parameter. If `NULL` then the default values from `params_fr_wei()` are used.
`fr_method, fr_wei_method`	character string with valid `method` argument for `fitdist_fr()` and `fitdist_fr_wei()` respectively.
`do_shiny_progress`	logical indicating whether to send progress updates to a running shiny app, using the `shiny::withProgress()` and `shiny::incProgress()` methods. This function only calls `shiny::incProgress()` and assumes the `shiny::withProgress()` has already bee initialized.
`verbose`	logical indicating whether to print verbose output.
`...`	additional arguments are ignored.

This function is a wrapper around fitdist_fr() and fitdist_fr_wei(), which iterates through a wide range of possible thresholds to determine the fit parameters, and associated lower and upper bounds. The results are intended to be plotted to determine appropriate thresholds to use when calculating the lower and upper bounds for barcodes and genes in a single cell RNA-seq dataset.

list with one element for each value in count_vector, where each list element contains a list with one entry for each value in argument dists containing the fit parameters for each selected distribution, as well as an entry "min_count" which contains the minimum counts to use in each fit. When dists contains "frechet-weibull" each list includes "lower_bound". When dists contains "frechet" each list includes "upper_bound". The output is intended to be passed to get_salsa_table().

Other SALSA core functions: get_salsa_table

library(salsa);
data(oz2_numi_per_cell);
x <- oz2_numi_per_cell$count[oz2_numi_per_cell$count >= 16];
x_salsa <- do_salsa_steps(x,
   count_vector=c(16,32,128),
   cache_fr=NULL,
   cache_fr_wei=NULL);
x_df <- get_salsa_table(x_salsa);
x_df;