olapuentesantana / easier_manuscript Goto Github PK

(1) An error occurs because the list name of the model by cancer type of "sysdata.rda" you provided and the list name of the model used in function "predict_imune_response".

(2) If possible, can I see an example of an output from function "predict_imune_response"?

I have a problem loading normalized TCGA data as a matrix to compute_pathways_scores function.

I would be interested in these two questions overall:

1. Is it possible to get examples of the input and output?
2. What does exactly the function predict_patients_response return? Is it indication stable disease (SD), Partial Response (PR) etc.?

trained_models[[any_cancer_type]] %>% names()
[1] "pathways" "immunecells" "tfs" "lrpairs"
[5] "ccpairs"

in predict_immune_response view names

  views <- c(Pathways.cor = 'gaussian',
             ImmuneCells = 'gaussian',
             TFs = 'gaussian',
             LRpairs.spec.pc = 'gaussian',
             CCpairsGroupedScores.spec.pc = 'gaussian')

The following error occurs because the "view_name" of trained_models and the "view_name "of predictions_immune_response do not match.

Error in array(STATS, dims[perm]) : 
  'data' must be of a vector type, was 'NULL'

Also,

Even if the above predict_immune_response "view names" are modified to those of trained_models and proceeded, in "predict_with_multitaskelasticnet",

Error in matrix(as.matrix(Intercept), nrow = ncol(Slope), ncol = nrow(x.test[[1]])) :
  I get the same error as non-numeric matrix extent.

my R version

> version
               _                           
platform       aarch64-apple-darwin20      
arch           aarch64                     
os             darwin20                    
system         aarch64, darwin20           
status                                     
major          4                           
minor          1.0                         
year           2021                        
month          05                          
day            18                          
svn rev        80317                       
language       R                           
version.string R version 4.1.0 (2021-05-18)
nickname       Camp Pontanezen    

If possible, can you provide Docker images in which the easler works well?

I follow your install instruction and also install dependency packages ‘progeny’, ‘viper’ and ‘dorothea’ , but i still can not install it properly!
library(devtools)
install_github("olapuentesantana/easier_manuscript")

• installing source package ‘easier’ ...
  ** using staged installation
  ** R
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded from temporary location
  Error: package or namespace load failed for ‘easier’ in namespaceExport(ns, exports):
  undefined exports: compute_CC_pairs, compute_CCpair_pval
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing ‘/home/ldp/miniconda2/envs/R4.0.3/lib/R/library/easier’
  Error: Failed to install 'easier' from GitHub:

i found some internal Rdata files were used in easier, for example:

load("data/cor_genes_ICB_proxies.RData")
load("data/IPS_genes.RData")
load("data/list_top100pathways_responsive_genes.RData")
load("data/Ligand_Receptors_Rdata/intercell.network.CC.pairs.grouped.cancer.spec.RData")
load("data/resistance.program.RData")
load("data/grouping_lrpairs_features_info.RData")
load("data/TCGA_mean_sd.RData")

where can I get access to these R.Data files???

LR_pairs_weights <- compute_LR_pairs(RNA.tpm=C4_tpm_exp_mat,

•                                 remove.genes.ICB_proxies=FALSE,
  

•                                 compute.cytokines.pairs=FALSE,
  

•                                 cancertype="pancan")
  

Error in compute_LR_pairs(RNA.tpm = C4_tpm_exp_mat, remove.genes.ICB_proxies = FALSE, :
object 'intercell.network.cancer.spec' not found