TIMER_deconv function inputs

[annavpo]

Could you please explain the structure of the inputs : curated.cell.types and sig and/or provide an example of each input?
Thank you!

TIMER_deconv <- function(mix,ref,curated.cell.types,sig) from TIMER_codes.R

[haijingjin]

Could you please explain the structure of the inputs : curated.cell.types and sig and/or provide an example of each input?
Thank you!

TIMER_deconv <- function(mix,ref,curated.cell.types,sig) from TIMER_codes.R

• Mix is the mixture data for deconvolution analysis (N by J, N for gene number, J for mixture sample number).
• Ref is the reference profile (N by J', N for gene number, J' for reference sample number)
• curated.cell.types.sig is a length-J' vector of reference annotation. The content of vector is the reference sample name, and the name of the vector is the cell type identity.
• sig is a vector containing signature gene names.
  Other issues:
• curated.cell.types might be confusing, please look into http://cistrome.org/TIMER/codes/CancerImmunePipeline.R for the construction of this annotation object. I recommend you directly refer to their code and play with the corresponding data they provided.
• This is just a customized code for our benchmark analysis. For the optimal performance, please contact TIMER team.