filter_genes: this function returns a table of interesting genes based on...

In tmirus/TTT: What the Package Does (One Line, Title Case)

Description

this function returns a table of interesting genes based on lasso model fit, specificity and differential expression

Usage

filter_genes(
  differential.genes,
  entropies,
  lasso.data = NULL,
  deg.weight = 2,
  lls.weight = 3,
  entropy.weight = 1,
  build.lasso = FALSE,
  gamma = 3,
  ncores = 4,
  counts = NULL,
  ids = NULL,
  verbose = TRUE
)

Arguments

differential.genes	data frame containing information about differential expression of genes
entropies	named numeric vector of entropies for all genes
lasso.data	output of build_lassos function; default NULL
deg.weight	weight of p-value in overall gene ranking; default 2
lls.weight	weight of lasso fit in overall gene ranking; default 3
entropy.weight	weight of entropy in overall gene ranking; default 1
build.lasso	logical, if lasso.data is NULL, should lasso models be calculated? default FALSE
gamma	numeric > 0, if build.lasso is TRUE, the gamma value passed to build_lassos; default 3
ncores	numeric > 0, the number of cores available for calculation; only used for lasso building, default 4
counts	non-negative numeric matrix containing gene counts, rows correspond to spots, columns correspond to genes
ids	data frame or matrix assigning spatial coordinates to the spots (see process_input() for details)
verbose	logical, default TRUE

Value

data frame containing gene name, cluster with lowest p-value, lowest p-value, up/downregulation information, lls fit (if lasso data was supplied) and entropy for each gene

tmirus/TTT documentation built on April 17, 2021, 11:04 p.m.