`R/custom_deconvolution_methods.R`

`deconvolute_cibersort_custom.Rd`

Deconvolute using CIBERSORT or CIBERSORT abs and a custom signature matrix.

```
deconvolute_cibersort_custom(
gene_expression_matrix,
signature_matrix,
QN = FALSE,
absolute = FALSE,
abs_method = "sig.score",
...
)
```

- gene_expression_matrix
a m x n matrix with m genes and n samples

- signature_matrix
a m x l matrix with m genes and l cell types. The matrix should contain only a subset of the genes useful for the analysis.

- QN
boolean. Wheter to quantile normalize the data. Data should be normalized when the signature matrix is derived from different studies/sample batches

- absolute
Set to TRUE for CIBERSORT absolute mode.

- abs_method
Choose method to compute absolute score (only if

`absolute=TRUE`

).- ...
passed through to the original CIBERSORT function. A native argument takes precedence over an immunedeconv argument (e.g.

`QN`

takes precedence over`arrays`

). Documentation is not publicly available. Log in to the CIBERSORT website for details.

the gene expression and the signature matrix should be provided in the same normalization