get_signature_matrix_options: Creation of the options of the "get signature matrix" docker...
In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

get_signature_matrix_options

R Documentation

Creation of the options of the "get signature matrix" docker command

Description

Creation of the options of the "get signature matrix" docker command

Usage

get_signature_matrix_options(
  refsample,
  g_min = 300,
  g_max = 500,
  q_value = 0.01,
  filter = FALSE,
  k_max = 999,
  remake = FALSE,
  replicates = 5,
  sampling = 0.5,
  fraction = 0.75
)

Arguments

`refsample`	The filename of the single cell data.
`g_min`	Minimum number of genes per cell type in sig. matrix.
`g_max`	Maximum number of genes per cell type in sig. matrix.
`q_value`	Q-value threshold for differential expression.
`filter`	Remove non-hematopoietic genes.
`k_max`	Maximum condition number. Will be added to the file name.
`remake`	Remake signature gene matrix.
`replicates`	Number of replicates to use for building scRNAseq reference file.
`sampling`	Fraction of available single cell GEPs selected using random sampling.
`fraction`	Fraction of cells of same identity showing evidence of expression.