CIBERSORT_rel_F: CIBERSORT_rel_F

In margenomics/Deconvolution: Deconvolution graphs

CIBERSORT_rel_F

Description

Function that generates the relative deconvolution plot with the CIBERSORT method, with the fractional plot, and returns a df resulting from the deconvolution.

Usage

CIBERSORT_rel_F(
  matrix,
  sig.matrix,
  fractions,
  results_dir,
  height = 10,
  name = FALSE
)

Arguments

matrix	expression matrix, this matrix must be in .txt format, organized in tabulated columns with one column containing the list of genes, with the name Gene.symbol, Gene.Symbol or Geneid, and in the rest of the columns the names of the samples and the expression values for the genes. (Example. Counts.HUMAN_nodup_Sal_Veh_IPs_INPUTs.txt).
sig.matrix	Signature matrix, this matrix must be in .txt format, organized in tabulated columns with one column containing the list of genes, with the name Gene.symbol, Gene.Symbol or Geneid, and in the rest of the columns the cell types and the expression values for the genes. (Example. Monaco-ABIS_Immune11_Microarray.txt).
fractions	Vector that identifies the fractions of the sample list to be used to fractionate the samples in different graphs.
results_dir	Directory to which the graphics will be generated.
height	Number that defines the height of the graph, to increase or decrease the height, which has a default value of 10.
name	Alternative name for the chart, which by default has the structure Sig_type_method.matrixName_Plot.png (Example. "graph_1")

Value

Returns the generated graphs and the df of the deconvolution.

Author(s)

Nidia Barco Armengol

Examples

CIBERSORT_rel_F("Counts.HUMAN_nodup_Sal_Veh_IPs_INPUTs.txt", "Monaco-ABIS_Immune11_Microarray.txt", f, results_dir = "/bicoh/nidia/Deconv/Brain_MMartin/test", height= 8, name= "MONACO")

margenomics/Deconvolution documentation built on March 19, 2022, 5:44 a.m.