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

get_cell_fractions_options

R Documentation

Creation of the options of the "get cell fractions" docker command

Description

Creation of the options of the "get cell fractions" docker command

Usage

get_cell_fractions_options(
  sigmatrix,
  mixture,
  rmbatch_B_mode = FALSE,
  rmbatch_S_mode = FALSE,
  perm = 0,
  label = "none",
  refsample = NULL,
  source_GEPs = sigmatrix,
  qn = FALSE,
  absolute = FALSE,
  abs_method = "sig.score"
)

Arguments

`sigmatrix`	The filename of the signature matrix.
`mixture`	The filename of the bulk expression data.
`rmbatch_B_mode`	Run B-mode batch correction (default: FALSE).
`rmbatch_S_mode`	Run S-mode batch correction (default: FALSE).
`perm`	No. of permutations for p-value calculation (default: 0).
`label`	The label which will be added to the file name. Default is "none", adding no label at all.
`refsample`	The filename of the single cell data.
`source_GEPs`	<file_name> Signature matrix GEPs for batch correction (default: sigmatrix).
`qn`	Run quantile normalization (default: FALSE).
`absolute`	Run absolute mode (default: FALSE).
`abs_method`	Pick absolute method ("sig.score" (default) or "no.sumto1").